16-176718-T-A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate

The NM_000558.5(HBA1):​c.2T>A​(p.Met1?) variant causes a start lost 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 pathogenic (★).

Frequency

Genomes: not found (cov: 28)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

HBA1
NM_000558.5 start_lost

Scores

7
6
3

Clinical Significance

Likely pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 2.48
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PVS1
Start lost variant, no new inframe start found.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 16-176718-T-A is Pathogenic according to our data. Variant chr16-176718-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2573442.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HBA1NM_000558.5 linkuse as main transcriptc.2T>A p.Met1? start_lost 1/3 ENST00000320868.9 NP_000549.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HBA1ENST00000320868.9 linkuse as main transcriptc.2T>A p.Met1? start_lost 1/31 NM_000558.5 ENSP00000322421 P1
HBA1ENST00000472694.1 linkuse as main transcriptn.21T>A non_coding_transcript_exon_variant 1/21
HBA1ENST00000397797.1 linkuse as main transcriptc.-46T>A 5_prime_UTR_variant 1/32 ENSP00000380899
HBA1ENST00000487791.1 linkuse as main transcript upstream_gene_variant 1

Frequencies

GnomAD3 genomes
Cov.:
28
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
6.88e-7
AC:
1
AN:
1453242
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
722450
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.02e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
28

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

alpha Thalassemia Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpJun 27, 2023Variant summary: HBA1 c.2T>A (p.Met1Lys) alters the initiation codon and is predicted to result either in absence of the protein or truncation of the encoded protein due to translation initiation at a downstream codon. An alternative downstream in-frame start codon (Met33) is located in the encoded protein. An activation of potential downstream translation at this initiation site would result in a shortened protein missing the first 32 amino acids from the protein sequence. At least one pathogenic missense variant has been reported upstream of this alternate codon in ClinVar. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 230058 control chromosomes (gnomAD). c.2T>A has been reported in the literature as a homozygous and as a heterozygous genotype in individuals suspected of alpha thalassemia and in the heterozygous state in alpha thalassemia trait carriers presenting with mild microcytosis and hypochromia (e.g. Waye_2016, Keikhaei_2018). These reports do not provide unequivocal conclusions about association of the variant with Alpha Thalassemia. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported, however another variant affecting the initiation codon (c.2T>G, p.Met1Arg) has been classified as pathogenic in ClinVar. The following publications have been ascertained in the context of this evaluation (PMID: 29627922, 28865746, 27821014). No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.30
D
BayesDel_noAF
Pathogenic
0.20
CADD
Uncertain
24
DANN
Uncertain
0.98
DEOGEN2
Uncertain
0.63
D
Eigen
Benign
0.069
Eigen_PC
Benign
0.065
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Uncertain
0.90
D
M_CAP
Pathogenic
0.92
D
MetaRNN
Pathogenic
0.99
D
MetaSVM
Uncertain
0.74
D
MutationTaster
Benign
1.0
D;D
PROVEAN
Uncertain
-3.6
D
REVEL
Pathogenic
0.90
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Vest4
0.91
MutPred
0.98
Loss of stability (P = 0.0065);
MVP
0.99
ClinPred
0.99
D
GERP RS
3.3
Varity_R
0.96
gMVP
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1316527998; hg19: chr16-226717; API