rs35328027

chr11-5225872-A-Cchr11-5225872-A-G

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.316-146T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000168 in 596,488 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000017 (0 hom.)
• Consequence: HBB NM_000518.5 intron
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: -0.111

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 11-5225872-A-C is Pathogenic according to our data. Variant chr11-5225872-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 36312.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5225872-A-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBB	NM_000518.5	c.316-146T>G		intron_variant		ENST00000335295.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBB	ENST00000335295.4	c.316-146T>G		intron_variant		1	NM_000518.5	P1
HBB	ENST00000647020.1	c.316-146T>G		intron_variant				P1
HBB	ENST00000633227.1	c.*132-146T>G		intron_variant, NMD_transcript_variant		3
HBB	ENST00000475226.1	n.248-146T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000168 AC: 1 AN: 596488 Hom.: 0 AF XY: 0.00000314 AC XY: 1 AN XY: 318522

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000272

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

beta Thalassemia Pathogenic:2

Pathogenic, no assertion criteria provided	curation	The ITHANET community portal, The Cyprus Institute of Neurology and Genetics	Nov 25, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 12, 2018	Variant summary: HBB c.316-146T>G (Legacy Name: IVS-II-705 (T->G)) is located at a position not widely known to affect splicing. However, several computational tools predict a significant impact on normal splicing: Three predict the variant strengthens a cryptic 5' donor site and one predicts the variant creates a 3' acceptor site. Gorman_1998 states "In the thalassemic IVS2705 human b-globin gene, a T-to-G mutation at position 705 of intron 2 improves the match of the surrounding sequence to the consensus donor splice site (ACTGAT/GTAAGA to ACTGAG/GTAAGA; / indicates the splice site). In the transcribed IVS2705 pre-mRNA, the presence of this new 5' splice site activates an acceptor splice site 126 nt upstream, resulting in incorrectly spliced b-globin mRNA containing a fragment of the intron (Fig. 1A). This fragment creates a premature stop codon resulting in a truncated b-globin polypeptide." Multiple functional studies support these predictions (Dobkin_1983, Spenc_1982, and Gorman_1998). The variant was absent in 30972 control chromosomes (gnomAD). The variant, c.316-146T>G, has been reported in the literature in individuals affected with Beta Thalassemia Intermedia. These data indicate that the variant may be associated with disease. A ClinVar submission (evaluation after 2014) from a clinical diagnostic laboratory classifies the variant as "pathogenic." Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 29, 2023	The HBB c.316-146T>G variant has been reported in the published literature in individuals with beta-thalassemia trait (PMID: 29251008 (2018)) and in trans with another pathogenic HBB variant in an individual with beta(+) thalassemia (PMID: 30843739 (2019)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	May 10, 2022	The c.316-146T>G variant (also known as IVS-II-705 (T->G), rs35328027, HbVar ID: 890) has been reported in a patient diagnosed with beta(+) thalassemia (Spence 1982). This variant is reported in ClinVar (Variation ID: 36312) and is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This is an intronic variant in a moderately conserved nucleotide, and computational analyses (Alamut v.2.11) predict that this variant may impact splicing by creating a novel cryptic donor splice site. Functional characterization of the mRNA transcript indicate that the variant causes the utilization of a cryptic splice acceptor 126 nucleotides upstream, leading to the inclusion of sequences from intron 2 of HBB (Dobkin 1983). Based on the above information, the variant is classified as pathogenic. References: HbVar link: https://globin.bx.psu.edu/hbvar/hbvar.html Dobkin C et al. Abnormal splice in a mutant human beta-globin gene not at the site of a mutation. Proc Natl Acad Sci U S A. 1983. 80(5):1184-8. PMID: 6298782. Spence S et al. Five nucleotide changes in the large intervening sequence of a beta globin gene in a beta+ thalassemia patient. Nucleic Acids Res. 1982. 10(4):1283-94. PMID: 6280138. -

Beta-plus-thalassemia Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 01, 1983

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.2
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.90		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.90		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs35328027; hg19: chr11-5247102;