rs35699606

Positions:

• chr11-5226994-A-AC

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1 PP5

The NM_000518.5(HBB):​c.27_28insG​(p.Ser10ValfsTer14) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,613,172 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. K9K) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.00011 (2 hom., cov: 32)
  • Exomes 𝑓: 0.00013 (0 hom.)
• Consequence: HBB NM_000518.5 frameshift
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:23 U:1 O:1
• Conservation: PhyloP100: 3.53

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 Likely_pathogenic. Variant got 9 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 353 pathogenic variants in the truncated region.
• PP5: Variant 11-5226994-A-AC is Pathogenic according to our data. Variant chr11-5226994-A-AC is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 36308.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=20, not_provided=1, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBB	NM_000518.5	c.27_28insG	p.Ser10ValfsTer14	frameshift_variant	1/3	ENST00000335295.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBB	ENST00000335295.4	c.27_28insG	p.Ser10ValfsTer14	frameshift_variant	1/3	1	NM_000518.5	P1

Frequencies

GnomAD3 genomes AF: 0.000105 AC: 16 AN: 152194 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00332

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000251 AC: 63 AN: 251192 Hom.: 0 AF XY: 0.000317 AC XY: 43 AN XY: 135748

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00203

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000133 AC: 194 AN: 1460860 Hom.: 0 Cov.: 33 AF XY: 0.000194 AC XY: 141 AN XY: 726824

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00212

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.00e-7

Gnomad4 OTH exome AF: 0.000133

GnomAD4 genome AF: 0.000105 AC: 16 AN: 152312 Hom.: 2 Cov.: 32 AF XY: 0.000188 AC XY: 14 AN XY: 74492

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00332

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000756

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:23 Uncertain:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

beta Thalassemia Pathogenic:10 Other:1

Pathogenic, no assertion criteria provided	curation	The ITHANET community portal, The Cyprus Institute of Neurology and Genetics	Nov 25, 2019	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 03, 2022	The p.Ser10Valfs*14 variant in HBB is a well-known pathogenic variant associated with autosomal recessive beta-Thalassemia (selected references Kazazian 1984 PMID: 6714226, Villegas 1998 PMID: 9949622, Jalilian 2017 PMID: 283917585). This variant has been reported in ClinVar (Variation ID 36308) and was identified in 16/4826 South Asian chromosomes by gnomAD (https://gnomad.broadinstitute.org). This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 10 and leads to a premature termination codon 14 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Loss of function of the HBB gene is an established disease mechanism in autosomal recessive beta thalassemia. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive beta thalassemia. ACMG/AMP Criteria applied: PM2_Supporting, PVS1, PM3_Strong. -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 19, 2019	NM_000518.4(HBB):c.27dupG(S10Vfs*14) is classified as pathogenic in the context of Hb beta chain-related hemoglobinopathy; it is associated with beta thalassemia and is classified as a beta-zero variant. Sources cited for classification include the following: PMID 22110956, 9949622, 24369358, 6714226, 16821247 and 21509314. Classification of NM_000518.4(HBB):c.27dupG(S10Vfs*14) is based on the following criteria: The variant causes a premature termination codon that is expected to be targeted by nonsense-mediated mRNA decay and is reported in individuals with the relevant phenotype. Please note: this variant was assessed in the context of healthy population screening. -
Pathogenic, criteria provided, single submitter	clinical testing;curation	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 18, 2011	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Mar 17, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetic Diagnostics Department, Viafet Genomics Laboratory	Mar 25, 2021	Viafet Genomics Laboratory has identified this variant in one homozygous and three compound heterozygous individuals affected with Beta-Thalassemia. In addition, this variant was reported in 26 individuals, as part of Carrier Screening testing, who were not affected with this condition. -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	May 22, 2022	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.025%). Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000036308 / PMID: 6714226). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	Jan 27, 2016	The c.27dupG (p.Ser10Valfs*14) frameshift variant in the HBB gene is a well-known variant associated with autosomal recessive Beta-Thalassemia (Baysal, 2005; Sinha et al., 2009; Al-Gazali et al., 2010; Ankala et al., 2015). This variant is predicted to cause a protein termination in exon 1 (out of a total of 3 exons in the coding sequence). Frameshift variants have been described in the HBB gene in several affected individuals and are, therefore, a common mechanism of disease. This variant is located upstream of two heme binding sites and two 2,3-biphosphoglycerate binding sites, and thus, the truncated protein would lack these important binding sites. This c.27dupG has been reported at low frequency in the control population databases (Exome Sequencing Project [ESP] = NA, 1000 Genomes = NA, and ExAC = 0.206%). In silico algorithms predict the resulting transcript will be targeted for the Nonsense Mediated Decay (NMD) Pathway. Therefore, this collective evidence supports the classification of the c.27dupG (p.Ser10Valfs*14) as a recessive Pathogenic variant for Beta-Thalassemia. -
Pathogenic, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	-	- -

not provided Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 29, 2022	Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 22975760, 27453201, 28635337, 6714226, 8537236, 9949622, 28391758, 27263053) -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	May 28, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2023	HBB: PM3:Very Strong, PVS1, PM2:Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 13, 2023	The HBB c.27dup; p.Ser10ValfsTer14 variant (also known as Ser9fs when numbered from the mature protein or as Codons 8/9 (+G), rs35699606, HbVar ID: 786) has been reported in individuals with beta (0) thalassemia, both in the homozygous state and in trans to another pathogenic variant (Jalilian 2017, Kazazian 1984, Muhammad 2017, HbVar database and references therein). Consistent with reports that it is prevalent in affected individuals of South Asian descent (Jalilian 2017, Kazazian 1984, Muhammad 2017), this variant is found in the South Asian population with an overall allele frequency of 0.2% (62/30614 alleles) in the Genome Aggregation Database. This variant causes a frameshift by duplicating a single nucleotide, so it is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, this variant is considered to be pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/hbvar.html Jalilian M et al. The Frequency of HBB Mutations Among Beta-Thalassemia Patients in Hamadan Province, Iran. Hemoglobin. 2017 Jan;41(1):61-64. PMID: 28391758. Kazazian HH Jr et al. Molecular characterization of seven beta-thalassemia mutations in Asian Indians. EMBO J. 1984 Mar;3(3):593-6. PMID: 6714226. Muhammad R et al. Population-Based Genetic Study of Beta-Thalassemia Mutations in Mardan Division, Khyber Pakhtunkhwa Province, Pakistan. Hemoglobin. 2017 Mar;41(2):104-109. PMID: 28635337. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 12, 2023	This sequence change creates a premature translational stop signal (p.Ser10Valfs*14) in the HBB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HBB are known to be pathogenic (PMID: 23637309). This variant is present in population databases (rs35699606, gnomAD 0.2%). This premature translational stop signal has been observed in individual(s) with autosomal recessive beta thalassemia (PMID: 9949622, 27263053, 28391758, 28635337). This variant is also known as CD8/9 (+G), codon 8/9 (+G), FSC 8/9 (+G), and c.27_28insG. ClinVar contains an entry for this variant (Variation ID: 36308). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -

HBB-related disorder Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Feb 26, 2024	The HBB c.27dupG variant is predicted to result in a frameshift and premature protein termination (p.Ser10Valfs*14). This variant (which also may be referred to as c.27_28insG) has been previously reported to be causative for beta-thalassemia (Kazazian et al. 1984. PubMed ID: 6714226; Giardine et al. 2014. PubMed ID: 24137000; Jalilian et al. 2017. PubMed ID: 28391758; Muhammad et al. 2017. PubMed ID: 28635337). This variant is reported in 0.20% of alleles in individuals of South Asian descent in gnomAD. Frameshift variants in HBB are expected to be pathogenic. This variant is interpreted as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 28, 2017	The HBB c.27dupG (p.Ser10ValfsTer14) variant results in a frameshift and is predicted to result in premature termination of the protein. The p.Ser10ValfsTer14 variant, also known as cd8/9+G, is a well-described pathogenic variant. Across a selection of the available literature the p.Ser10ValfsTer14 variant has been reported in at least 229 disease alleles in individuals with HBB-related disorders, including in at least 38 patients in a homozygous state and 30 patients in a compound heterozygous state. The zygosity of the remaining alleles is not known (Kazazian et al. 1984; Villegas et al. 1998; Ansari et al. 2011; Hoppe et al 2013; El-Shanshory et al. 2014; Yasmeen et al. 2016). The variant is reported at frequencies from 1% to 47% depending on the ethnic background but is more common in the South Asian and Middle Eastern populations (Lahiry et al. 2008; Ansari et al. 2011). Control data are unavailable for the p.Ser10ValfsTer14 variant, which is reported at a frequency of 0.00206 in the South Asian population of the Exome Aggregation Consortium. Based on the potential impact of frameshift variants and the supporting evidence from the literature, the p.Ser10ValfsTer14 variant is classified as pathogenic for HBB-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Beta-thalassemia HBB/LCRB Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The frame shift (p.Ser10ValfsTer14) variant has been observed in numerous individuals and families affected with Thalassemia-beta, dominant inclusion-body and has been reported as a prevalent disease-associated variant in several populations (Muhammad et. al., 2017; Villegas et. al., 1998, Jalilian et. al., 2017). The p.Ser10ValfsTer14 variant is novel (not in any individuals) in 1000 Genomes and has allele frequency of 0.002508% in gnomAD database. This variant has been reported to the ClinVar database as Pathogenic. This variant causes a frameshift starting with codon Serine 10, changes this amino acid to Valine residue, and creates a premature Stop codon at position 14 of the new reading frame, denoted p.Ser10ValfsTer14. It is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic. In the absence of another reportable variant, the molecular diagnosis of beta thalassemia is not confirmed. -
Pathogenic, criteria provided, single submitter	clinical testing	Lifecell International Pvt. Ltd	-	The frameshift duplication NM_000518.5 (HBB):c.27dupG (p.Ser10Valfs*14) has been reported to ClinVar as Pathogenic with a status of (2 stars) criteria provided, multiple submitters, no conflicts (Variation ID 36308 as of 2022-06-02). The p.Ser10Valfs*14 variant is observed in 62/30,614 (0.2025%) alleles from individuals of gnomAD South Asian background in gnomAD. The p.Ser10Valfs*14 variant is novel (not in any individuals) in 1kG. This variant is predicted to cause loss of normal protein function through protein truncation caused a frameshift mutation. The frame shifted sequence continues 14 residues until a stop codon is reached. This variant is a frameshift variant which occurs in an exon of HBB upstream of where nonsense mediated decay is predicted to occur. This variant has been previously classified as pathogenic, indicating that the region is critical to protein function. There are 83 downstream pathogenic loss of function variants, with the furthest variant being 123 residues downstream of this variant. This indicates that the region is critical to protein function. The p.Ser10Valfs*14 vari ant is a loss of function variant in the gene HBB, which is intolerant of Loss of Function variants, as indicated by the presence of existing pathogenic loss of function variant NP_000509.1:p.M1L and 61 others. This premature translational stop signal has been observed in individual(s) with autosomal recessive beta thalassemia and loss of function in HBB is known to be pathogenic (Muhammad R et al., 2017). For these reasons, this variant has been classified as Pathogenic. -

Beta zero thalassemia Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Feb 27, 2017

- -

alpha Thalassemia;C0002895: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

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 08, 2021

- -

Hb SS disease Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

-

- -

Malaria, susceptibility to Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

Mar 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs35699606; hg19: chr11-5248224;