11-5226925-C-G

Position:

• chr11-5226925-C-G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PP3_Strong PP5_Very_Strong

The NM_000518.5(HBB):​c.92+5G>C variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000292 in 1,612,226 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.00024 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00030 (1 hom.)
• Consequence: HBB NM_000518.5 splice_donor_5th_base, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:30 O:1
• Conservation: PhyloP100: 2.72

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.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 11-5226925-C-G is Pathogenic according to our data. Variant chr11-5226925-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 15447.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5226925-C-G is described in Lovd as [Pathogenic]. Variant chr11-5226925-C-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBB	NM_000518.5	c.92+5G>C		splice_donor_5th_base_variant, intron_variant		ENST00000335295.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBB	ENST00000335295.4	c.92+5G>C		splice_donor_5th_base_variant, intron_variant		1	NM_000518.5	P1

Frequencies

GnomAD3 genomes AF: 0.000237 AC: 36 AN: 152190 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00726

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000593 AC: 149 AN: 251204 Hom.: 0 AF XY: 0.000803 AC XY: 109 AN XY: 135754

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: 0.00474

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000881

Gnomad OTH exome AF: 0.000489

GnomAD4 exome AF: 0.000297 AC: 433 AN: 1459918 Hom.: 1 Cov.: 33 AF XY: 0.000439 AC XY: 319 AN XY: 726420

Gnomad4 AFR exome AF: 0.0000598

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00471

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.01e-7

Gnomad4 OTH exome AF: 0.000365

GnomAD4 genome AF: 0.000243 AC: 37 AN: 152308 Hom.: 1 Cov.: 32 AF XY: 0.000389 AC XY: 29 AN XY: 74474

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00747

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000288 Hom.: 0

Bravo AF: 0.0000416

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:30 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

beta Thalassemia Pathogenic:10 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Suma Genomics	-	- -
Pathogenic, no assertion criteria provided	curation	The ITHANET community portal, The Cyprus Institute of Neurology and Genetics	Nov 25, 2019	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	May 20, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 11, 2016	Variant summary: The c.92+5G>C variant affects a non-conserved intronic nucleotide. Mutation taster predicts damaging outcome for this variant. 4/5 programs in Alamut predict a loss of canonical splicing donor site. ESE finder predicts that this variant may affect ESE site of SC35. This variant is found in 87/121280 control chromosomes at a frequency of 0.0007173, which does not exceed maximal expected frequency of a pathogenic allele (0.0111803). This variant has been reported in many affected individuals (both homozygotes and compound heterozygotes with another disease variant in trans) presented with phenotypes including BTHAL-MJR and BTHAL-ITM. Functional studies proved the aberrant RNA splicing products (Treisman_Nature_1983). In addition, multiple reputable databases classified this variant as pathogenic. Taken together, this variant was classified as a Pathogenic. -
Pathogenic, flagged submission	clinical testing	Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital	Mar 10, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Sep 01, 2022	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.053%). Splice region variant. Functional studies provide moderate evidence that the variant has a damaging effect on the gene or gene product (PMID: 6188062). In silico tools predict the variant to alter splicing and produce an abnormal transcript (SpliceAI: 0.82). The homozygous variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000015447). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Nov 12, 2019	NM_000518.4(HBB):c.92+5G>C(aka IVS-I-5) is classified as pathogenic in the context of Hb beta chain-related hemoglobinopathy and is associated with beta thalessemia. Sources cited for classification include the following: PMID: 6714226, 6188062, 19000664, 18294253, and 23348723. Classification of NM_000518.4(HBB):c.92+5G>C(aka IVS-I-5) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
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	Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	Dec 13, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 03, 2022	The c.92+5G>C variant in HBB has been reported, in the homozygous and compound heterozygous state, in numerous individuals with beta thalassemia major and beta thalassemia intermedia (selected references Kazazian 1984 PMID: 6714226, Muhammad 2017 PMID: 28635337, https://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=824). It has been reported in ClinVar (Variation ID 15447) and has been identified in 35/4822 South Asian chromosomes by gnomAD (https://gnomad.broadinstitute.org). This variant is located in the 5' splice region. Computational tools predict a splicing impact and functional studies have shown it reduces or completelys deactivate the natural splice donor site in intron 1 and activates three cryptic splice donor sites (Treisman 1983 PMID: 6188062). Different splice variants at this residue (c.92+5G>A, c.92+5G>T) have been reported as pathogenic in ClinVar. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive beta thalassemia. ACMG/AMP Criteria applied: PM2_Supporting,PP3, PS3_Moderate, PM3_very strong. -

not provided Pathogenic:8

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jul 10, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 25, 2024	This sequence change falls in intron 1 of the HBB gene. It does not directly change the encoded amino acid sequence of the HBB protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs33915217, gnomAD 0.5%), and has an allele count higher than expected for a pathogenic variant. This variant has been observed in individuals with beta thalassemia (PMID: 18294253, 19000664, 22392582, 23162295, 27263053). It is commonly reported in individuals of Pakistani and Indian ancestry (PMID: 18294253, 19000664, 22392582, 23162295, 27263053). This variant is also known as IVS-I-5, IVSI-5, and IVS1-5. ClinVar contains an entry for this variant (Variation ID: 15447). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 6188062). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 22, 2021	Reported in association with beta thalassemia major and beta thalassemia intermedia when in the homozygous or compound heterozygous state, opposite of a second HBB variant (Kazazian et al., 1984; Baysal, et al., 2011; Al-Allawi et al., 2013; Chaudhary et al., 2016).; Non-canonical splice site variant demonstrated to reduce or completely deactivate the natural splice donor site in intron 1 and activate three cryptic splice donor sites (Treisman et al., 1983; Divoky et al., 1992); Different splice variants at this residue (c.92+5G>A; c.92+5G>T) have been reported as pathogenic in ClinVar and at GeneDx (ClinVar SCV# 15449; 15448; ClinVar); This variant is associated with the following publications: (PMID: 6188062, 23348723, 22975760, 6585831, 31714438, 25525159, 1463768, 6714226, 23826747, 20301599, 22074124, 27134826, 23234478, 27690257, 20132300, 19000664, 18294253, 27263053, 2004023, 16291734, 14576320, 28635337, 29651865, 31589614, 31890591, 9163586) -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 13, 2023	The HBB c.92+5G>C variant (rs33915217, HbVar ID: 824), also known as IVS-I-5 (G->C), is reported in the literature in the homozygous and compound heterozygous state in multiple individuals affected with severe beta(+) thalassemia (Cheng 1984, Muhammad 2017, Panja 2016, Perea 2004, Yasmeen 2016, HbVar database and references therein). This variant is reported as pathogenic by multiple laboratories in ClinVar (Variation ID: 15447), and it is found in the South Asian population with an allele frequency of 0.47% (145/30,612 alleles) in the Genome Aggregation Database. Functional studies demonstrate that the variant causes aberrant splicing, leading to a significant reduction in full-length mRNA (Triesman 1983). Based on available information, the c.92+5G>C variant is considered to be pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/hbvar.html Cheng T et al. Beta-Thalassemia in Chinese: use of in vivo RNA analysis and oligonucleotide hybridization in systematic characterization of molecular defects. Proc Natl Acad Sci U S A. 1984 81(9):2821-5. PMID: 6585831 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 Panja A et al. Hb Midnapore beta53(D4)Ala>Val; HBB: c.161C>T: A Novel Hemoglobin Variant with a Structural Abnormality Associated with IVS-I-5 (G>C) (HBB: c.92+5G>C) Found in a Bengali Indian Family. Hemoglobin. 2016 Sep;40(5):300-303. PMID: 27690257 Perea FJ Molecular spectrum of beta-thalassemia in the Mexican population. Blood Cells Mol Dis. 2004 Sep-Oct;33(2):150-2. PMID: 15315794 Treisman R et al. Specific transcription and RNA splicing defects in five cloned beta-thalassaemia genes. Nature. 1983 302(5909):591-6. PMID: 6188062 Yasmeen H et al. The molecular characterization of Beta globin gene in thalassemia patients reveals rare and a novel mutations in Pakistani population. Eur J Med Genet. 2016 Aug;59(8):355-62. PMID: 27263053 -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 23, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	May 12, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jun 28, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital	Dec 17, 2022	- -

Beta-thalassemia HBB/LCRB Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The splice region c.92+5G>C variant in HBB gene has been reported in homozygous or compound heterozygous state in individuals affected with beta thalassemia (Yasmeen et al. 2016). The c.92+5G>C variant is reported with the allele frequency of 0.06% in the gnomAD Exomes. This variant has been reported to the ClinVar database as Pathogenic (multiple submissions). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing, and studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (Treisman et al. 1983). For these reasons, this variant has been classified as Pathogenic. In the absence of another reportable variant in the HBB gene, the molecular diagnosis is not confirmed. -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The splice region c.92+5G>C variant in HBB gene has been reported previously in homozygous or compound heterozygous state in individual(s) affected with beta thalassemia (Yasmeen H et al., 2016). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (Treisman R et al., 1983). This variant is reported with the allele frequency of 0.05% in the gnomAD Exomes and novel in 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic by multiple submitters. This splice region variant in intron 1 affects the position five nucleotides downstream of exon 1. For these reasons, this variant has been classified as Pathogenic. In the absence of another reportable variant in HBB gene, the molecular diagnosis is not confirmed. -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Aug 09, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Lifecell International Pvt. Ltd	-	A Homozygote Splice site region variant c.92+5G>C in Exon 1 of the HBB gene that results in the amino acid substitution was identified. The observed variant has a maximum allele frequency of 0.00059/0.00006% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic (variant ID: 15447). This variant has previously been reported for beta-thalassemia by Treisman R, et, al., 1983. Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. -

Beta-plus-thalassemia Pathogenic:2

Pathogenic, no assertion criteria provided	research	College of Science, Al Muthanna University, Al Muthanna University	Jan 01, 2018	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	May 01, 1984	- -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 13, 2017

The c.92+5G>C intronic pathogenic mutation results from a G to C substitution 5 nucleotides after coding exon 1 in the HBB gene. This mutation has been detected in individuals with beta-thalassemia (Agarwal S et al. Int J Lab Hematol, 2010 Jun;32:369-72; Sivalingam M et al. Int J Lab Hematol, 2012 Aug;34:377-82; Sirdah MM et al. Blood Cells Mol. Dis., 2013 Apr;50:247-51). In addition, this mutation showed reduced splicing efficiency with approximately half of the amount of RNA compared to wild type (Treisman R et al. Nature, 1983 Apr;302:591-6). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

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

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Malaria, susceptibility to Pathogenic:1

Pathogenic, criteria provided, single submitter

research

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

Mar 17, 2024

- -

Beta-thalassemia major Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

Feb 16, 2021

- -

Hb SS disease Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

-

- -

Hereditary persistence of fetal hemoglobin Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Neuberg Centre For Genomic Medicine, NCGM

-

The missense c.92+5G>C variant in HBB gene has been reported in heterozygous state in multiple individuals affected with Beta thalassemia (Hidayati NI, et. al., 2020; Yasmeen H,et. al., 2016). Functional studies demonstrate that the variant has a damaging effect on the gene or gene product (Treisman R, et. al.,1983). The c.92+5G>C variant is reported with an allele frequency of 0.05% in the gnomAD exomes database and is novel (not in any individuals) in 1000 Genomes database. This variant has been reported to the ClinVar database as Pathogenic (multiple submissions). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	20
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.99
SpliceAI score (max)		0.82		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.43		Position offset: 21
DS_DL_spliceai		0.82		Position offset: 5

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

Publications

LitVar

Other links and lift over

dbSNP: rs33915217; hg19: chr11-5248155;