11-5225923-G-A

Position:

• chr11-5225923-G-A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2 PP3_Moderate PP5_Very_Strong

The NM_000518.5(HBB):​c.316-197C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000046 in 152,110 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: 𝑓 0.000046 (0 hom., cov: 32)
• Consequence: HBB NM_000518.5 intron
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:10 O:1
• Conservation: PhyloP100: -0.616

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
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 11-5225923-G-A is Pathogenic according to our data. Variant chr11-5225923-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 15458.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5225923-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HBB	NM_000518.5	c.316-197C>T		intron_variant		ENST00000335295.4	NP_000509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HBB	ENST00000335295.4	c.316-197C>T		intron_variant		1	NM_000518.5	ENSP00000333994	P1
HBB	ENST00000647020.1	c.316-197C>T		intron_variant				ENSP00000494175	P1
HBB	ENST00000633227.1	c.*132-197C>T		intron_variant, NMD_transcript_variant		3		ENSP00000488004
HBB	ENST00000475226.1	n.248-197C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0000460 AC: 7 AN: 152110 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0000460 AC: 7 AN: 152110 Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4 AN XY: 74314

Gnomad4 AFR AF: 0.0000483

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000688 Hom.: 0

Bravo AF: 0.0000831

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 24, 2023	The c.316-197C>T variant (also known as IVS-II-654 C->T, rs34451549, HbVar ID:889) has been reported in the compound heterozygous state in individuals with beta (+) thalassemia intermedia and in the homozygous state in a patient with transfusion-dependent beta-thalassemia major (see link to HbVar database and references therein, Lin 2013, Wu 2017). This variant is reported as pathogenic in ClinVar (Variation ID: 15458) and is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This is an intronic variant, and computational algorithms (Alamut v.2.11) predict that this variant impacts splicing by creating a novel cryptic donor splice site. Additionally, functional mRNA studies of this variant demonstrate aberrant splicing that leads to the production of a transcript that contains a premature termination codon (Cheng 1984, Huang 1994). Based on available information, this variant is considered 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 Huang SZ et al. RNA transcripts of the beta-thalassaemia allele IVS-2-654 C-->T: a small amount of normally processed beta-globin mRNA is still produced from the mutant gene. Br J Haematol. 1994 Nov;88(3):541-6. PMID: 7819066 Lin M et al. Hemoglobinopathy: molecular epidemiological characteristics and health effects on Hakka people in the Meizhou region, southern China. PLoS One. 2013;8(2):e55024. PMID: 23383304 Wu L et al. B-thalassemia caused by compound heterozygous mutations and cured by bone marrow transplantation: A case report. Mol Med Rep. 2017 Nov;16(5):6552-6557. PMID: 28901454 -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 15, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Nov 06, 2023	Published functional studies demonstrate a damaging effect as cDNA sequencing of c.316-197C>T revealed the use of a new cryptic donor site, resulting in a transcript with exons 1,2,3, and nucleotides 580-652 of intron 3; this transcript corresponds to the major species identified by blot hybridization analysis of erythroid RNA of affected patients (PMID: 6585831); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 26201722, 26086873, 27469621, 26084319, 21228398, 28943547, 30275481, 22975760, 20412082, 6585831, 26290351, 26865073, 23806067, 22335963, 20642335, 27117566, 25412720, 28901454, 31124576, 10222649, 9163586, 8091935, 8161731, 2143120, 28674233, 33092414) -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 21, 2024	This sequence change falls in intron 2 of the HBB gene. It does not directly change the encoded amino acid sequence of the HBB protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C-terminus of the protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with beta-thalassemia (PMID: 2014803, 6585831, 8435318, 29695942). It has also been observed to segregate with disease in related individuals. This variant is also known as IVS2+654C>T, IVS-II-654 (C>T). ClinVar contains an entry for this variant (Variation ID: 15458). Studies have shown that this variant results in inclusion of 73 nucleotides from intron 2 and introduces a new termination codon (PMID: 6585831). However the mRNA is not expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

beta Thalassemia Pathogenic:2 Other:1

Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Mar 17, 2017	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 09, 2019	NM_000518.4(HBB):c.316-197C>T 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-plus variant. Sources cited for classification include the following: PMID 2014803, 6585381 and 8435318. Classification of NM_000518.4(HBB):c.316-197C>T 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. -

Beta zero thalassemia Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

May 01, 1984

- -

HBB-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 20, 2023

The HBB c.316-197C>T variant is predicted to interfere with splicing. This variant, previously described as IVS2-654C>T, has been reported to alter splicing and be causative for beta thalassemia (Cheng et al 1984. PubMed ID: 6585831; Lin LI et al 1991. PubMed ID: 2014803; Kazazian HH Jr et al 1986. PubMed ID: 2875755 This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. -

Beta-thalassemia major Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing;curation

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Aug 18, 2011

- -

Hb SS disease Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.18
DANN	Benign	0.28

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.94		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.94		Position offset: 2

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

Publications

LitVar

Other links and lift over

dbSNP: rs34451549; hg19: chr11-5247153;