rs267607269

Positions:

• chr16-173515-C-G
• chr16-173515-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000517.6(HBA2):​c.344C>G​(p.Pro115Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P115L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 25)
• Consequence: HBA2 NM_000517.6 missense
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 0.262

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HBA2	NM_000517.6	c.344C>G	p.Pro115Arg	missense_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.344C>G	p.Pro115Arg	missense_variant	3/3	1	NM_000517.6	ENSP00000251595.6
HBA2	ENST00000482565.1	n.480C>G		non_coding_transcript_exon_variant	2/2	1
HBA2	ENST00000397806.1	c.248C>G	p.Pro83Arg	missense_variant	3/3	2		ENSP00000380908.1
ENSG00000290038	ENST00000702607.1	n.146G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 25

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

HBA2-related disorder Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 29, 2024

The HBA2 c.344C>G variant is predicted to result in the amino acid substitution p.Pro115Arg. This variant is also known as Hb Chiapas or p.Pro114Arg using legacy nomenclature. Individuals carrying this variant were described as clinically normal (Lisker et al. 1966. PubMed ID: 5945763; Jones et al. 1968. PubMed ID: 5650416; Ibarra et al. 1981. PubMed ID: 7319830). This variant has not been reported in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.20	D
BayesDel_noAF	Uncertain	0.050
CADD	Benign	18
DANN	Benign	0.97
DEOGEN2	Benign	0.14	.;T
Eigen	Benign	-0.66
Eigen_PC	Benign	-0.76
FATHMM_MKL	Benign	0.18	N
M_CAP	Pathogenic	0.57	D
MetaRNN	Uncertain	0.52	D;D
MetaSVM	Uncertain	0.25	D
PrimateAI	Uncertain	0.50	T
PROVEAN	Pathogenic	-6.3	D;D
REVEL	Uncertain	0.47
Sift	Uncertain	0.0090	D;D
Sift4G	Benign	0.070	T;T
Vest4		0.25
MutPred		0.55		Loss of phosphorylation at T119 (P = 0.1732);.;
MVP		0.98
MPC		1.4
ClinPred		0.75	D
GERP RS		1.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3
gMVP		0.90

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: rs267607269; hg19: chr16-223514;