chr16-173694-A-G

Position:

• chr16-173694-A-G

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 8P and 1B. PP5_Very_Strong BP4

The NM_000517.6(HBA2):​c.*94A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,383,378 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 25)
  • Exomes 𝑓: 0.000011 (1 hom.)
• Consequence: HBA2 NM_000517.6 3_prime_UTR
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:7 U:1 O:1
• Conservation: PhyloP100: 1.56

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 (HGNC:):

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PP5: Variant 16-173694-A-G is Pathogenic according to our data. Variant chr16-173694-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 375749.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HBA2	NM_000517.6	c.*94A>G		3_prime_UTR_variant	3/3	ENST00000251595.11	NP_000508.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HBA2	ENST00000251595.11	c.*94A>G		3_prime_UTR_variant	3/3	1	NM_000517.6	ENSP00000251595.6
HBA2	ENST00000397806.1	c.*94A>G		3_prime_UTR_variant	3/3	2		ENSP00000380908.1
HBA2	ENST00000482565.1	n.*19A>G		downstream_gene_variant		1
ENSG00000290038	ENST00000702607.1	n.-34T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome AF: 0.0000108 AC: 15 AN: 1383378 Hom.: 1 Cov.: 23 AF XY: 0.00000870 AC XY: 6 AN XY: 689444

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: 0.0000124

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000379

Gnomad4 OTH exome AF: 0.0000525

GnomAD4 genome Cov.: 25

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7 Uncertain:1 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 14, 2022	The HBA2 c.*94A>G variant (rs63751269, HbVar ID: 1070), also known as Poly A (A->G) or Hb T-Saudi, is reported in the literature in both homozygous individuals with an Hb H disease phenotype, and heterozygous carriers who were borderline microcytic and hypochromic without a significant anemia (Thein 1988, Yavarian 2005, HbVar and references therein). In addition, this variant has been observed in individuals affected with Hb H disease that also carried the pathogenic alpha -3.7 deletion (Yavarian 2005). The c.*94A>G variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant is predicted to disrupt the conserved polyadenylation signal and result in an elongated transcript. Consistent with these predictions, functional assays indicate a disruption of normal transcriptional termination and transcript polyadenylation both in cultured cells and in patient samples, resulting in reduced levels of the mature mRNA (Higgs 1983, Whitelaw 1986). Based on available information, this variant is considered to be pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Higgs DR et al. Alpha-thalassaemia caused by a polyadenylation signal mutation. Nature. 1983 Nov 24-30;306(5941):398-400. PMID: 6646217. Thein SL et al. The polyadenylation site mutation in the alpha-globin gene cluster. Blood. 1988 Feb;71(2):313-9. PMID: 3337900. Whitelaw E et al. Alpha-thalassaemia caused by a poly(A) site mutation reveals that transcriptional termination is linked to 3' end processing in the human alpha 2 globin gene. EMBO J. 1986 Nov;5(11):2915-22. PMID: 3024968. Yavarian M et al. Molecular basis of Hb H disease in southwest Iran. Hemoglobin. 2005;29(1):43-50. PMID: 15768554. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Feb 01, 2023	Published functional studies demonstrate a damaging effect; specifically, the variant disrupts normal transcriptional termination and transcript polyadenylation and results in reduced levels of mature mRNA and HBA2 gene expression (Higgs et al., 1983; Whitelaw et al., 1986); In silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Variant aliases include: T, T-Saudi , poly A1 , PA-1; This variant is associated with the following publications: (PMID: 25370869, 16103716, 20301608, 28385057, 24826794, 29032940, 22686351, 19205971, 11480787, 1281602, 6646217, 3024968, 34272389, 29627922) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Dec 01, 2020	This variant interferes with polyadenylation of the alpha-2 globin mRNA and causes the synthesis of an extended alpha-2 globin mRNA transcript (PMID: 6646217 (1983), 3024968 (1986), and HbVar (http://globin.bx.psu.edu/cgi-bin/hbvar/counter)). The c.*94A>G variant is associated with alpha-thalassemia. Homozygosity for this variant is associated with Hb H disease (PMID: 7701914 (1994), 20507641 (2010), 25370869 (2014)). -

alpha Thalassemia Pathogenic:2 Other:1

not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City	Aug 25, 2019	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Dec 30, 2017	- -

beta Thalassemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 03, 2022

The c.*94A>G variant in HBA2, also known as Poly A (A->G) or Hb T-Saudi, has been reported in several (both homozygous as well as compound heterozygous (with a pathogenic variant in trans))individuals with an Hb H disease phenotype, and heterozygous carriers who were borderline microcytic and hypochromic without a significant anemia (Fei 1992 PMID: 1281602, Adekile 1994 PMID: 7701914, Thein 1988 PMID: 3337900, Yavarian 2005 PMID: 15768554, HbVar: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=1070 ). It has also been reported in ClinVar (Variation ID375749) and was absent from large population databases. This variant is predicted to disrupt the conserved polyadenylation signal and result in an elongated transcript. In vitro functional studies (both using cultured cells and patient samples) support an impact on protein function as they show a disruption of normal transcriptional termination and transcript polyadenylation, resulting in reduced levels of the mature mRNA (Higgs 1983 PMID: 6646217, Whitelaw 1986 PMID: 3024968). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Hb H disease. ACMG/AMP Criteria applied: PM3 Very strong, PM2_supporting, PS3_Moderate, PP3). -

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

Jan 10, 2022

- -

Hemoglobin H disease Uncertain:1

Uncertain significance, flagged submission

clinical testing

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

Mar 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	17
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs63751269; hg19: chr16-223693;