rs41474145

chr16-173004-AGAGGT-A

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PVS1_Strong PP3 PP5_Very_Strong

The NM_000517.6(HBA2):c.95+2_95+6del variant causes a splice donor, coding sequence change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.00011 (0 hom., cov: 3)
  • Exomes 𝑓: 0.00029 (10 hom.)
  • Failed GnomAD Quality Control
• Consequence: HBA2 NM_000517.6 splice_donor, coding_sequence
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:7 O:1
• Conservation: PhyloP100: 9.03

Genes affected

HBA2 (HGNC:4824): (hemoglobin subunit alpha 2) The human alpha globin gene cluster located on chromosome 16 spans about 30 kb and includes seven loci: 5'- zeta - pseudozeta - mu - pseudoalpha-1 - alpha-2 - alpha-1 - theta - 3'. The alpha-2 (HBA2) and alpha-1 (HBA1) coding sequences are identical. These genes differ slightly over the 5' untranslated regions and the introns, but they differ significantly over the 3' untranslated regions. Two alpha chains plus two beta chains constitute HbA, which in normal adult life comprises about 97% of the total hemoglobin; alpha chains combine with delta chains to constitute HbA-2, which with HbF (fetal hemoglobin) makes up the remaining 3% of adult hemoglobin. Alpha thalassemias result from deletions of each of the alpha genes as well as deletions of both HBA2 and HBA1; some nondeletion alpha thalassemias have also been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 13 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.3053613 fraction of the gene. Cryptic splice site detected, with MaxEntScore 5.8, offset of -19, new splice context is: atgGTgcgg. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
• PP5: Variant 16-173004-AGAGGT-A is Pathogenic according to our data. Variant chr16-173004-AGAGGT-A is described in ClinVar as [Pathogenic]. Clinvar id is 375746.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-173004-AGAGGT-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBA2	NM_000517.6	c.95+2_95+6del		splice_donor_variant, coding_sequence_variant	1/3	ENST00000251595.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBA2	ENST00000251595.11	c.95+2_95+6del		splice_donor_variant, coding_sequence_variant	1/3	1	NM_000517.6	P1
HBA2	ENST00000484216.1	c.64+2_64+6del		splice_donor_variant, coding_sequence_variant	1/2	1
HBA2	ENST00000482565.1	n.116_120del		non_coding_transcript_exon_variant	1/2	1
HBA2	ENST00000397806.1	c.-2+51_-2+55del		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1 AN: 9452 Hom.: 0 Cov.: 3 FAILED QC

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: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00549

GnomAD3 exomes AF: 0.000294 AC: 16 AN: 54504 Hom.: 0 AF XY: 0.000255 AC XY: 7 AN XY: 27454

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000817

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000164

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000147

Gnomad OTH exome AF: 0.00155

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000292 AC: 128 AN: 439000 Hom.: 10 AF XY: 0.000290 AC XY: 67 AN XY: 231172

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000693

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000617

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000167

Gnomad4 OTH exome AF: 0.000319

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000106 AC: 1 AN: 9420 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 4366

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00549

Alfa AF: 0.000223 Hom.: 0

Bravo AF: 0.0000793

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

alpha Thalassemia Pathogenic:3 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Dec 05, 2022	The HBA2 c.95+2_95+6del variant is classified as Pathogenic (PVS1, PS4, PP4) The HBA2 c.95+2_95+6del variant is located in a splice donor region. Computational predictions support a deleterious effect on splicing and a likely disruption of the protein reading frame and non-sense mediated decay of the resulting protein product (PVS1). This pentanucleotide HBA2:c.95+2_95+6delTGAGG deletion occurs within the 5' splice junction of the first intervening sequence, preventing normal RNA splicing. This mutation is listed on the Haemoglobin Variant Database as an alpha thalassaemia mutation (PMID: 7151175) (PS4). Present in numerous internal database patients as per alamut with consistent symptoms of alpha thalassaemia carrier. No functional studies performed. The clinical features of this case are highly specific for HBA1/2, and this patient has a well-defined syndrome with little overlap with other clinical presentations (PP4). Variants in HBA1/2 are highly specific for alpha thalassaemia. The variant has been reported in dbSNP (rs41474145) and has been reported as Pathogenic by other diagnostic laboratories (ClinVar Variation ID: 375746). It has been reported in HGMD (CD810004). -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 10, 2024	The c.95+2_95+6del variant in HBA2 is a common pathogenic variant for alpha thalassemia in the Mediterranean region (Felber 1982 PMID: 7151175, Lacerra 2004 PMID: 15365991, Orkin 1981 PMID: 6946451, HbVar database: https://globin.bx.psu.edu/hbvar/menu.html; HbVarID:1065). This variant has been reported by other clinical laboratories in ClinVar (Variation ID 375746) and was absent from large population studies (gnomAD, v.3.1.2). This deletion affects the canonical splice site position (+2) and is predicted to cause altered splicing leading to an abnormal or absent protein. Biallelic loss of function of the HBA2 gene is an established disease mechanism in autosomal recessive alpha thalassemia. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive alpha thalassemia. ACMG/AMP Criteria applied: PVS1_Strong, PM3_Strong, PM2_supporting. -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Aug 17, 2017	- -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 31, 2023	The HBA2 c.95+2_95+6del variant (HbVar ID: 1065) is a common pathogenic alpha thalassemia variant that disrupts the canonical splice donor site of intron 1 and alters splicing (Felber 1982, Lacerra 2004, Orkin 1981, see HbVar link). Heterozygosity for this variant is predicted to result in silent carrier status. Based on the information available, this variant is considered to be pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Felber BK et al. Abnormal RNA splicing causes one form of alpha thalassemia. Cell. 1982 Jul;29(3):895-902. PMID: 7151175. Lacerra G et al. Sequence variations of the alpha-globin genes: scanning of high CG content genes with DHPLC and DG-DGGE. Hum Mutat. 2004 Oct;24(4):338-49. PMID: 15365991. Orkin SH et al. Mutation in an intervening sequence splice junction in man. Proc Natl Acad Sci U S A. 1981 Aug;78(8):5041-5. PMID: 6946451. -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Sep 30, 2020	The c.95+2_95+6delTGAGG pathogenic variant in the alpha2-globin (HBA2) gene is the deletion of nucleotides 2 to 6 (TGAGG) of intron 1. This deletion occurs in the splice-donor site and prevents normal splicing of the alpha2-globin mRNA (see , and PMIDs: 6946451 (1981), 7151175 (1982), and 20507641 (2010)), and has been reported in individuals affected with alpha thalassemia in the published literature (PMIDs: 6946451 (1981), 7151175 (1982), 15365991 (2004), and 29115104 (2018)). An in vitro study reports no functional alpha-globin protein is synthesized from the mutant alpha2-globin allele (PMID: 7151175 (1982)). -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 18, 2022	Common variant reported in individuals of Mediterranean ethnicity with HbH disease (Orkin et al., 1981; Mesbah-Amroun et al., 2008; Farra et al., 2014; de la Fuent-Gonzalo et al., 2019); Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Also denoted as IVS1-5nt and alpha-Hph due to alternative nomenclature; This variant is associated with the following publications: (PMID: 6946451, 15365991, 26771086, 31025160, 7151175, 25284125, 18473243, 23215864, 31589614, 29627922) -

alpha Thalassemia;C0700299:Heinz body anemia;C3161174:Hemoglobin H disease;C4693823:Erythrocytosis, familial, 7 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Feb 24, 2022

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41474145; hg19: chr16-223003;