rs41321345
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2PM4PP5_Very_Strong
The NM_000517.6(HBA2):c.428A>C(p.Ter143SerextTer31) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: not found (cov: 25)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
HBA2
NM_000517.6 stop_lost
NM_000517.6 stop_lost
Scores
3
4
Clinical Significance
Conservation
PhyloP100: 1.21
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]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Stoplost variant in NM_000517.6 Downstream stopcodon found after 154 codons.
PP5
Variant 16-173599-A-C is Pathogenic according to our data. Variant chr16-173599-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 15627.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBA2 | NM_000517.6 | c.428A>C | p.Ter143SerextTer31 | stop_lost | 3/3 | ENST00000251595.11 | NP_000508.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HBA2 | ENST00000251595.11 | c.428A>C | p.Ter143SerextTer31 | stop_lost | 3/3 | 1 | NM_000517.6 | ENSP00000251595 | P1 | |
HBA2 | ENST00000482565.1 | n.564A>C | non_coding_transcript_exon_variant | 2/2 | 1 | |||||
ENST00000702607.1 | n.62T>G | non_coding_transcript_exon_variant | 1/1 | |||||||
HBA2 | ENST00000397806.1 | c.332A>C | p.Ter111SerextTer31 | stop_lost | 3/3 | 2 | ENSP00000380908 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 genomes
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25
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248882Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134862
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459116Hom.: 0 Cov.: 33 AF XY: 0.00000276 AC XY: 2AN XY: 725626
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GnomAD4 genome Cov.: 25
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25
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:3Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 18, 2021 | The Hb Koya Dora variant (HBA2: c.428A>C; p.Ter143SerextTer31 also known as Ter142Ser when numbered from the mature protein, rs41321345) is reported in the heterozygous state associated with mild anemia and hypochromia (see link to HbVar). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant abolishes the canonical termination codon, resulting in an elongated protein that is unstable, similar to other stop loss variants (Hb Constant Spring, Hb Icaria)(see HbVar links and references therein). Based on available information, this variant is considered to be pathogenic. References: Link to HbVar database for Hb Koya Dora: https://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=705&.cgifields=histD Link to HbVar database for Hb Constant Spring: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=703&.cgifields=histD Link to HbVar database for Hb Icaria: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=704&.cgifields=histD - |
Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Aug 03, 2022 | This variant disrupts the translation stop codon of the HBA2 mRNA and is predicted to cause HBA2 protein elongation. The frequency of this variant in the general population, 0.000004 (1/248882 chromosomes, http://gnomad.broadinstitute.org), is consistent with pathogenicity. In the published literature, the variant has been associated with alpha-thalassemia (PMIDs: 26365411 (2015), 19373587 (2009), 1802886 (1991), 1155453 (1975)). Based on the available information, this variant is classified as pathogenic. - |
alpha Thalassemia Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Neuberg Centre For Genomic Medicine, NCGM | - | The stop lost c.428A>C p.Ter143SerextTer31 variant in the HBA2 gene has been reported in compound heterozygous state in a patient with Alpha-thalassemia Deshpande, Prashant et al., 2015. This variant is reported with the allele frequency 0.0004% in the gnomAD Exomes and novel in 1000 Genomes. The variant is reported to ClinVar as Pathogenic. The p.Ter143SerextTer31 variant in the stop codon Ter/* at position 143, changing it to a Serine-codon a no-stop variant and adding a tail of new amino acids to the protein’s C-terminus, ending at a new stop codon Ter/* at position 31. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. The amino acid change p.Ter143SerextTer31 in HBA2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. Functional studies are required to prove the pathogenicity of the variant. For these reasons, this variant has been classified as Likely Pathogenic. - |
HEMOGLOBIN KOYA DORA Other:1
other, no assertion criteria provided | literature only | OMIM | Mar 28, 2013 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
N;N
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at