rs281864566

chr16-176931-T-Achr16-176931-T-Cchr16-176931-T-G

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2 PM5 PP3 PP5

The NM_000558.5(HBA1):c.98T>A(p.Met33Lys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M33I) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 30)
• Consequence: HBA1 NM_000558.5 missense, splice_region
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:1
• Conservation: PhyloP100: 1.31

Genes affected

HBA1 (HGNC:4823): (hemoglobin subunit alpha 1) 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 Likely_pathogenic. Variant got 6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr16-176932-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 3075901.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 16-176931-T-A is Pathogenic according to our data. Variant chr16-176931-T-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1330794.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Pathogenic=1}. Variant chr16-176931-T-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBA1	NM_000558.5	c.98T>A	p.Met33Lys	missense_variant, splice_region_variant	2/3	ENST00000320868.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBA1	ENST00000320868.9	c.98T>A	p.Met33Lys	missense_variant, splice_region_variant	2/3	1	NM_000558.5	P1
HBA1	ENST00000472694.1	n.234T>A		non_coding_transcript_exon_variant	1/2	1
HBA1	ENST00000487791.1	n.67T>A		splice_region_variant, non_coding_transcript_exon_variant	2/2	1
HBA1	ENST00000397797.1	c.2T>A	p.Met1?	start_lost, splice_region_variant	2/3	2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 13

GnomAD4 genome Cov.: 30

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Mar 26, 2021

The Hb Queens Park variant (HBA1: c.98T>A; p.Met33Lys, also known as Met32Lys when numbered from the mature protein, rs281864566) is reported in the literature in an individual with microcytic anemia who also carries the –alpha3.7 deletion (Phylipsen 2010, see HbVar Hb Queens Park link). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The methionine at codon 33 is highly conserved, and computational analyses (REVEL: 0.835) predict that this variant is deleterious. Additionally, variants at this residue occur in a region important for alpha-beta globin contacts and are not usually detected by HPLC and thus are considered unstable (Brennan 2017, Harteveld 2005). Furthermore, a different variant at this codon (p.Met33Ile) is reported in individuals with microcytic anemia and is considered to be disease-causing (Brennan 2017, Harteveld 2005, see HbVar Hb Amsterdam-A1 link). Based on available information, the Hb Queens Park variant is considered to be pathogenic. References: HbVar link to Hb Amsterdam-A1: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=3126&.cgifields=histD HbVar link to Hb Queens Park: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=2784&.cgifields=histD Brennan SO et al. Hb Amsterdam-A1 (a32(B13)Met?Ile; HBA1: c.99G>A): A Hyperunstable Variant Due to a New Mutation on the a1 Gene. Hemoglobin. 2017 Mar;41(2):140-143. Harteveld CL et al. Hb Amsterdam (alpha32(B13)Met--Ile (alpha2)): a new unstable variant associated with an alpha-thalassemia phenotype and a new African polymorphism. Hemoglobin. 2005;29(4):257-62. Phylipsen M et al. Two new alpha1-globin gene point mutations: Hb Nedlands (HBA1:c.86C>T) (alpha28(B9)Ala-->Val) and Hb Queens Park (HBA1:c.98T>A) (alpha32(B13)Met-->Lys). Hemoglobin. 2010 Jan;34(2):123-6. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

May 25, 2023

Variant summary: HBA1 c.98T>A (p.Met33Lys), also referred to as Hb Queens Park, results in a non-conservative amino acid change located in the globin domain (IPR000971) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. This variant is also located near a canonical splice site and therefore could have an impact on normal RNA splicing: three computational tools predict the variant has no significant impact on splicing, whereas one predicts the variant slightly weakens the canonical 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 129824 control chromosomes (gnomAD). c.98T>A has been reported in the literature in two individuals together with the --SEA deletion, who were affected with a moderate microcytic-hypochromic anemia, and were positive for HbH inclusion bodies (Sroymora_2012, Viprakasit_2014), consistent with a (mild) HbH disease. In addition, the variant was also reported in trans with the -a3.7 deletion, in an individual who was affected with a mild microcytic-hypochromic anemia, without HbH inclusion bodies (Phylipsen_2010); this clinical picture is compatible with an alpha thalassemia trait (alpha thalassemia minor). Finally, the variant was also reported in silent carriers (He_2017, Tan_2021). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating this impact on protein function has been reported, however it has been suggested that the variant might result in an unstable protein, due to disrupting an amino acid that is important for alpha-beta globin contacts (Phylipsen_2010) or heme contact (Brennan_2017). In addition, other variants affecting the same amino acid (Met33Ile/Thr) have been reported in affected individuals (HGMD). The following publications have been ascertained in the context of this evaluation (PMID: 20353346, 22384838, 33439495, 24081251, 28125089, 28696843). One clinical diagnostic laboratory has submitted a clinical-significance assessment for this variant to ClinVar after 2014 and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_addAF	Pathogenic	0.47	D
BayesDel_noAF	Pathogenic	0.43
Cadd	Pathogenic	27
Dann	Benign	0.96
DEOGEN2	Benign	0.40	T;.
Eigen	Uncertain	0.47
Eigen_PC	Benign	0.17
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.92	D;D
M_CAP	Pathogenic	0.84	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Uncertain	0.57	D
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.54	T
PROVEAN	Uncertain	-3.8	D;D
REVEL	Pathogenic	0.83
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0010	D;D
Vest4		0.93
MutPred		0.92		Loss of stability (P = 9e-04);.;
MVP		1.0
ClinPred		0.99	D
GERP RS		0.77
Varity_R		0.97
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.53		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.53		Position offset: 2

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

Publications

LitVar

Other links and lift over

dbSNP: rs281864566; hg19: chr16-226930;