chr16-176771-G-C

Variant names:

• chr16-176771-G-C
• rs34504387
• NM_000558.5:c.55G>C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2 PP3 BP6_Moderate

The NM_000558.5(HBA1):​c.55G>C​(p.Gly19Arg) 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 Likely benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G19D) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 28)
• Consequence: HBA1 NM_000558.5 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1 O:1
• Conservation: PhyloP100: -0.0530

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 Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.782
• BP6: Variant 16-176771-G-C is Benign according to our data. Variant chr16-176771-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 15736.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HBA1	NM_000558.5	c.55G>C	p.Gly19Arg	missense_variant	Exon 1 of 3	ENST00000320868.9	NP_000549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBA1	ENST00000320868.9	c.55G>C	p.Gly19Arg	missense_variant	Exon 1 of 3	1	NM_000558.5	ENSP00000322421.5
HBA1	ENST00000472694.1	n.74G>C		non_coding_transcript_exon_variant	Exon 1 of 2	1
HBA1	ENST00000487791.1	n.24G>C		non_coding_transcript_exon_variant	Exon 1 of 2	1
HBA1	ENST00000397797.1	c.-2+9G>C		intron_variant	Intron 1 of 2	2		ENSP00000380899.1

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome Cov.: 27

GnomAD4 genome Cov.: 28

ClinVar

Significance: Likely benign

Submissions summary: Benign:1 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 05, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The HBA1 c.55G>C; p.Gly19Arg variant (Hb Handsworth, also known as Gly18Arg when numbered from the mature protein, rs34504387, ClinVar Variation ID 15736, HbVar ID: 22) has been reported as a stable hemoglobin and identified in the HBA2 gene of heterozygous individuals without clinically significant symptoms (Al Zadjali 2014, Griffiths 1977, see HbVar database and references therein). However, it has not been previously described in the literature in the HBA1 gene, and the phenotype of this variant in the presence of other alpha globin variants is unknown. This HBA1 variant is absent from the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.462). Based on available information, this variant is considered to be likely benign. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Al Zadjali S et al. Potential pitfalls in the diagnosis of Hb Handsworth in areas with high prevalence of HbS. Int J Lab Hematol. 2014 Aug;36(4):488-92. PMID: 24165563. Griffiths KD et al. Haemoglobin Handsworth alpha 18 (A16) glycine leads to arginne. FEBS Lett. 1977 Mar 15;75(1):93-5. PMID: 852596. -

HEMOGLOBIN HANDSWORTH Other:1

Jul 20, 2016

OMIM

Significance: other

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.59
BayesDel_addAF	Pathogenic	0.25	D
BayesDel_noAF	Uncertain	0.13
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.21	T
Eigen	Benign	-0.28
Eigen_PC	Benign	-0.40
FATHMM_MKL	Benign	0.55	D
LIST_S2	Benign	0.70	T
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.78	D
MetaSVM	Uncertain	0.40	D
PrimateAI	Uncertain	0.64	T
PROVEAN	Uncertain	-3.9	D
REVEL	Uncertain	0.46
Sift	Uncertain	0.0080	D
Sift4G	Benign	0.29	T
Vest4		0.65
MutPred		0.18		Gain of MoRF binding (P = 0.0187);
MVP		0.99
ClinPred		0.32	T
GERP RS		4.4
Varity_R		0.68
gMVP		0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs34504387; hg19: chr16-226770;