16-173004-AGAGGT-A

Position:

chr16-173004-AGAGGT-A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_StrongPP5_Very_Strong

The NM_000517.6(HBA2):c.95+2_95+6delTGAGG variant causes a splice donor, splice region, intron 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, splice_region, intron

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:8O:1

Conservation

PhyloP100: 9.03

Variant links:

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]

HBA2 links:

HBA2 (HGNC:):

HBA2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PVS1

Splicing +-2 bp (donor or acceptor) variant, product 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.

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	Protein	UniProt
HBA2	NM_000517.6 linkuse as main transcript	c.95+2_95+6delTGAGG		splice_donor_variant, splice_region_variant, intron_variant		ENST00000251595.11	NP_000508.1	P69905D1MGQ2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
HBA2	ENST00000251595.11 linkuse as main transcript	c.95+2_95+6delTGAGG	splice_donor_variant, splice_region_variant, intron_variant		1	NM_000517.6	ENSP00000251595.6	P69905
HBA2	ENST00000484216.1 linkuse as main transcript	c.62+2_62+6delTGAGG	splice_donor_variant, splice_region_variant, intron_variant		1		ENSP00000495899.1	A0A2R8Y7C0
HBA2	ENST00000482565.1 linkuse as main transcript	n.116_120delTGAGG	non_coding_transcript_exon_variant	1/2	1
HBA2	ENST00000397806.1 linkuse as main transcript	c.-2+51_-2+55delTGAGG	intron_variant		2		ENSP00000380908.1	G3V1N2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

9452

Hom.:

Cov.:

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:

AN:

54504

Hom.:

AF XY:

0.000255

AC XY:

AN XY:

27454

show subpopulations

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.:

AF XY:

0.000290

AC XY:

AN XY:

231172

show subpopulations

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:

AN:

9420

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

4366

show subpopulations

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.:

Bravo

AF:

0.0000793

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Pathogenic:4

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) -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Jul 31, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Aug 20, 2024	The HBA2 c.95+2_95+6del variant (rs41474145, HbVar ID: 1065, also known as alpha-thal-2 (-5nt) and IVS1 (-5nt)) is a common pathogenic alpha thalassemia variant and has been reported in heterozygous individuals with mild hypochromic microcytic anemia or silent carriers and in compound heterozygous individuals with alpha-thalassemia trait (Alhuthali 2023, Lacerra 2004, Orkin 1981, see HbVar link). This variant disrupts the canonical splice donor site of intron 1 and alters splicing (Felber 1982, Orkin 1981). 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 Alhuthali HM et al. Molecular patterns of alpha-thalassemia in the kingdom of Saudi Arabia: identification of prevalent genotypes and regions with high incidence. Thromb J. 2023 Nov 10;21(1):115. PMID: 37950286. 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	Dec 09, 2024	The HBA2 c.95+2_95+6del variant (also known as c.95+2_95+6delTGAGG and IVS1 (-5nt)) disrupts a canonical splice-donor site and interferes with normal HBA2 mRNA splicing (PMIDs: 6946451 (1981), 7151175 (1982), 20507641 (2010)). This variant has been reported in the published literature in multiple individuals including homozygous and compound heterozygous cases who were affected with alpha thalassemia or related conditions (PMIDs: 6946451 (1981), 7151175 (1982), 15365991 (2004), 29115104 (2018), 32893703 (2020), 38708170 (2024)). An in vitro study showed that no functional protein was synthesized from the mutant alpha2-globin allele (PMID: 7151175 (1982)). The frequency of this variant in the general population, 0.00082 (9/11036 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. -

alpha Thalassemia

Pathogenic:3Other:1

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. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Aug 17, 2017	- -
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). -

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

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over