NM_000517.6:c.46G>A

Variant names:

• chr16-172958-G-A
• rs281864811
• NM_000517.6:c.46G>A

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM5

The NM_000517.6(HBA2):​c.46G>A​(p.Gly16Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G16C) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 2)
  • Exomes 𝑓: 0.000028 (0 hom.)
• Consequence: HBA2 NM_000517.6 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.396
• Publications: 0 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: Uncertain_significance. The variant received 2 ACMG points.

• PM5: Other missense variant is known to change same aminoacid residue: Variant chr16-172958-G-T is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 1683493.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000517.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HBA2	NM_000517.6	MANE Select	c.46G>A	p.Gly16Ser	missense	Exon 1 of 3	NP_000508.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HBA2	ENST00000251595.11	TSL:1 MANE Select	c.46G>A	p.Gly16Ser	missense	Exon 1 of 3	ENSP00000251595.6
	HBA2	ENST00000484216.1	TSL:1	c.13G>A	p.Gly5Ser	missense	Exon 1 of 2	ENSP00000495899.1
	HBA2	ENST00000482565.1	TSL:1	n.65G>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 2

GnomAD2 exomes AF: 0.0000187 AC: 1 AN: 53380 AF XY: 0.0000372

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000127

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000283 AC: 11 AN: 388200 Hom.: 0 Cov.: 0 AF XY: 0.0000245 AC XY: 5 AN XY: 204132

African (AFR) AF: 0.00 AC: 0 AN: 9350

American (AMR) AF: 0.00 AC: 0 AN: 16892

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11932

East Asian (EAS) AF: 0.000424 AC: 11 AN: 25944

South Asian (SAS) AF: 0.00 AC: 0 AN: 43954

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24728

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1668

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 231608

Other (OTH) AF: 0.00 AC: 0 AN: 22124

GnomAD4 genome Cov.: 2

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions as Germline

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.081
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.15
CADD	Benign	16
DANN	Benign	0.84
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.21	N
M_CAP	Pathogenic	0.35	D
MetaRNN	Uncertain	0.73	D
MetaSVM	Benign	-0.60	T
PhyloP100		0.40
PrimateAI	Uncertain	0.66	T
PROVEAN	Benign	-0.050	N
REVEL	Uncertain	0.41
Sift	Benign	0.28	T
Sift4G	Benign	0.44	T
Vest4		0.70
MutPred		0.58		Gain of glycosylation at G16 (P = 0.0403)
MVP		0.99
MPC		1.3
ClinPred		0.029	T
GERP RS		-0.90
PromoterAI		-0.036	Neutral
gMVP		0.73
Mutation Taster		=41/59	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs281864811; hg19: chr16-222957;