rs374002189

chr16-172913-AT-A

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PS1_Moderate PP5_Very_Strong

The NM_000517.6(HBA2):c.2del(p.Met1?) variant causes a frameshift, start lost change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000074 (0 hom.)
• Consequence: HBA2 NM_000517.6 frameshift, start_lost
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 2.03

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 18 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 58 pathogenic variants in the truncated region.
• PS1: Another start lost variant in NM_000517.6 (HBA2) was described as [Likely_pathogenic] in ClinVar as 3075919
• PP5: Variant 16-172913-AT-A is Pathogenic according to our data. Variant chr16-172913-AT-A is described in ClinVar as [Pathogenic]. Clinvar id is 15692.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBA2	NM_000517.6	c.2del	p.Met1?	frameshift_variant, start_lost	1/3	ENST00000251595.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBA2	ENST00000251595.11	c.2del	p.Met1?	frameshift_variant, start_lost	1/3	1	NM_000517.6	P1
HBA2	ENST00000482565.1	n.21del		non_coding_transcript_exon_variant	1/2	1
HBA2	ENST00000397806.1	c.-46del		5_prime_UTR_variant	1/3	2
HBA2	ENST00000484216.1			upstream_gene_variant		1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000744 AC: 2 AN: 268920 Hom.: 0 Cov.: 0 AF XY: 0.00000698 AC XY: 1 AN XY: 143308

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000136

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Mar 26, 2021	The HBA2 c.2delT; p.Met1? variant (rs63750678), also known as initiation codon (-T), is reported in the literature in individuals affected with HbH disease who also carried a large deletion encompassing both the HBA1 and HBA2 genes on the other chromosome (see link to HbVar and references therein; Viprakasit 2005). This variant is reported in ClinVar (Variation ID: 15692), and abolishes the canonical initiation codon of HBA2, so it is predicted to result in an absent protein. Other variants that disrupt the initiation codon have been reported in individuals with alpha thalassemias and are considered pathogenic (Eng 2006, Olivieri 1987). Based on available information, the c.2delT; p.Met1? variant is considered to be pathogenic. References: Link to HbVar for Initiation codon (-T): http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=1062&.cgifields=histD Eng B et al. Three new alpha-thalassemia point mutations ascertained through newborn screening. Hemoglobin. 2006;30(2):149-53. Olivieri NF et al. An alpha-globin gene initiation codon mutation in a black family with HbH disease. Blood. 1987 Sep;70(3):729-32. Viprakasit V et al. A rare association of alphaO-thalassemia (--SEA) and an initiation codon mutation (ATG-->A-G) of the alpha2 gene causes Hb H disease in Thailand. Hemoglobin. 2005;29(3):235-40. -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 29, 2019	This variant is located in the translation initiation codon of the HBA2 mRNA and is predicted to interfere with HBA2 protein synthesis. It has been reported in an individual with Hb H disease in the published literature (PMID: 9322079 (1997)). -

alpha Thalassemia Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Natera, Inc.

Aug 31, 2018

- -

Hemoglobin H disease, nondeletional Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 2005

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs63750678; hg19: chr16-222912;