chr16-173266-C-A

Variant names:

• chr16-173266-C-A
• rs281860607
• NM_000517.6:c.237C>A

Variant summary

Our verdict is Likely pathogenic. The variant received 7 ACMG points: 8P and 1B. PM1 PM2 PP3_Strong BP6

The NM_000517.6(HBA2):​c.237C>A​(p.Asn79Lys) variant causes a missense 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. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Benign in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N79H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 7.4e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HBA2 NM_000517.6 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:1
• Conservation: PhyloP100: -7.80
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• alpha thalassemia spectrum

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
• erythrocytosis, familial, 7

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
• hemoglobin M disease

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Hb Bart's hydrops fetalis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin H disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Heinz body anemia

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
• methemoglobinemia, alpha type

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ENSG00000294455 (HGNC:):

ACMG classification

Our verdict: Likely_pathogenic. The variant received 7 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 5 benign, 12 uncertain in NM_000517.6
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.978
• BP6: Variant 16-173266-C-A is Benign according to our data. Variant chr16-173266-C-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 618159.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HBA2	NM_000517.6	c.237C>A	p.Asn79Lys	missense_variant	Exon 2 of 3	ENST00000251595.11	NP_000508.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBA2	ENST00000251595.11	c.237C>A	p.Asn79Lys	missense_variant	Exon 2 of 3	1	NM_000517.6	ENSP00000251595.6

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 7.39e-7 AC: 1 AN: 1352784 Hom.: 0 Cov.: 25 AF XY: 0.00000149 AC XY: 1 AN XY: 671368

African (AFR) AF: 0.00 AC: 0 AN: 26850

American (AMR) AF: 0.00 AC: 0 AN: 38082

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24914

East Asian (EAS) AF: 0.00 AC: 0 AN: 36864

South Asian (SAS) AF: 0.00 AC: 0 AN: 78384

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35644

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3900

European-Non Finnish (NFE) AF: 9.51e-7 AC: 1 AN: 1051782

Other (OTH) AF: 0.00 AC: 0 AN: 56364

GnomAD4 genome Cov.: 23

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:1 Benign:1

Jul 14, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Hb Stanleyville-II variant (HBA2: c.237C>G or c.237C>A; p.Asn79Lys, also known as Asn78Lys when numbered from the mature protein, rs281860607, HbVar ID: 119) is reported in individuals without any significant hematological symptoms and does not contribute to the clinical phenotype when found with other structural variants or pathogenic globin variants including HbS, Hb CS, and -3.7kb (Dherte 1959, Dode 1990, Kimura 2015, Lacerra 2004, Lin 2011, Moradkhani 2009, Pimentel 2011, Rhoda 1983, Schneider 1959, Silva 2012, Van Ros 1968, see HbVar database). This variant is reported in ClinVar (Variation ID: 618159) and is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. The asparagine at codon 79 is weakly conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.415). Based on available information, this variant is considered to be benign. References: Link to HbVar database for Hb-Stanleyville II: https://globin.bx.psu.edu/hbvar/hbvar.html Dherte P et al. Stanleyville I and II: two new variants of adult haemoglobin. Br Med J. 1959 Aug 29;2(5147):282-4. PMID: 13816361. Dode C et al. Locus assignment of human alpha globin mutations by selective amplification and direct sequencing. Br J Haematol. 1990 Oct;76(2):275-81. PMID: 2094330. Kimura EM et al. Investigating alpha-globin structural variants: a retrospective review of 135,000 Brazilian individuals. Rev Bras Hematol Hemoter. 2015 Mar-Apr;37(2):103-8. PMID: 25818820. 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. Lin M et al. Hb Stanleyville II [alpha 78(EF7) Asn?Lys] occurrence in combination with Hb Constant Spring. Blood Cells Mol Dis. 2011 Feb 15;46(2):145-6. PMID: 21093326. Moradkhani K et al. Mutations in the paralogous human alpha-globin genes yielding identical hemoglobin variants. Ann Hematol. 2009 Jun;88(6):535-43. PMID: 18923834. Pimentel FS et al. Homozygous Hb Stanleyville-II [alpha2 78(EF7) Asn>Lys; HBA2:c.237C>A, not C>G] associated with genotype -a 3.7/-a 3.7 in two Brazilian families. Int J Lab Hematol. 2011 Dec;33(6):566-9. PMID: 21470372. Rhoda MD et al. Sickle cell hemoglobin fiber formation strongly inhibited by the Stanleyville II mutation (alpha 78 Asn leads to Lys). Biochem Biophys Res Commun. 1983 Feb 28;111(1):8-13. PMID: 6681956. Schneider RG et al. A new haemoglobin variant in an American Negro. Br Med J. 1959 Aug 29;2(5147):285. PMID: 14443254. Silva et al. Hb Stanleyville-II [alpha78(EF7)Asn?Lys (alpha2); HbA2: c.237C>A]: incidence of 1:11,500 in a newborn screening program in Brazil. Hemoglobin. 2012;36(4):388-94. PMID: 22625430. Van Ros G et al. Haemoglobin Stanleyville II (alpha asparagine replaced by lysine). Br Med J. 1968 Oct 12;4(5623):92-3. PMID: 5696551. -

Oct 18, 2021

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The HBA2 c.237C>A (p.Asn79Lys) variant is reported in the published literature in individuals with hemoglobin abnormalities (PMID: 32597250 (2020)) and anemia (21470372 (2011), 22625430 (2012), 25109349 (2014), 33823095 (2021)). In the individuals with anemia, this variant occurred with the HB Constant Spring and alpha 3.7 deletion variants in HBA2 (PMIDs: 21093326 (2011), 22625430 (2012), 33823095 (2021)). It has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is benign or damaging. Based on the available information, we are unable to determine the clinical significance of this variant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Uncertain	0.032	T
BayesDel_noAF	Benign	-0.19
CADD	Benign	0.11
DANN	Benign	0.91
DEOGEN2	Benign	0.010	.;T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.080	N
M_CAP	Uncertain	0.17	D
MetaRNN	Pathogenic	0.98	D;D
MetaSVM	Benign	-0.59	T
PhyloP100		-7.8
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-1.2	N;N
REVEL	Uncertain	0.41
Sift	Uncertain	0.0090	D;D
Sift4G	Benign	0.10	T;T
Vest4		0.69
MutPred		0.94		Gain of ubiquitination at N79 (P = 0.0162);.;
MVP		0.98
MPC		1.5
ClinPred		0.11	T
GERP RS		-4.5
PromoterAI		-0.030	Neutral
gMVP		0.78
Mutation Taster		=6/94	disease causing

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

Other links and lift over

dbSNP: rs281860607; hg19: chr16-223265;