16-173540-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM1BP4_Moderate
The NM_000517.6(HBA2):c.369C>G(p.His123Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,607,450 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_000517.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HBA2 | NM_000517.6 | c.369C>G | p.His123Gln | missense_variant | 3/3 | ENST00000251595.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HBA2 | ENST00000251595.11 | c.369C>G | p.His123Gln | missense_variant | 3/3 | 1 | NM_000517.6 | P1 | |
HBA2 | ENST00000482565.1 | n.505C>G | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
ENST00000702607.1 | n.121G>C | non_coding_transcript_exon_variant | 1/1 | ||||||
HBA2 | ENST00000397806.1 | c.273C>G | p.His91Gln | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000740 AC: 11AN: 148608Hom.: 0 Cov.: 25
GnomAD3 exomes AF: 0.000157 AC: 39AN: 248160Hom.: 0 AF XY: 0.000134 AC XY: 18AN XY: 134542
GnomAD4 exome AF: 0.000125 AC: 183AN: 1458726Hom.: 3 Cov.: 33 AF XY: 0.000106 AC XY: 77AN XY: 725446
GnomAD4 genome ? AF: 0.0000740 AC: 11AN: 148724Hom.: 0 Cov.: 25 AF XY: 0.0000964 AC XY: 7AN XY: 72636
ClinVar
Submissions by phenotype
alpha Thalassemia Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Nov 29, 2022 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Apr 16, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 27, 2023 | The Hb Westmead variant (HBA2: c.369C>G; p.His123Gln, also known as His122Gln when numbered from the mature protein, rs41479347, HbVar ID: 185) has been reported in the heterozygous state in multiple individuals of East Asian descent, but has not been associated with significant clinical symptoms (Jiang 2020, Ma 2001, Viprakasit 2014, Wong 2004, HbVar database and references therein). This variant has been reported in homozygous individuals with mild anemia (Jiang 2020). However, it is an unstable hemoglobin variant, and its co-occurrence with beta thalassemia results in milder symptoms for the patient (Scheps 2020, Wong 2004, HbVar database and references therein). This variant is reported in ClinVar (Variation ID: 439771). It is found in the East Asian population with an overall allele frequency of 0.17% (33/19844 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.618). However, given the lack of clinical and functional data, the significance of the p.His123Gln variant is uncertain at this time. References: HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Jiang F et al. Hb Westmead (HBA2: c.369C>G): Hematological Characteristics in Heterozygotes with and without a0-Thalassemia. Hemoglobin. 2020 May;44(3):153-155. PMID: 32436451. Ma E et al. Interaction between (--SEA) alpha-thalassemia deletion and uncommon non-deletional alpha-globin gene mutations in Chinese patients. Haematologica. 2001; 86(5):539-40. PMID: 11410420. Scheps KG et al. Curating the gnomAD database: Report of novel variants in the globin-coding genes and bioinformatics analysis. Hum Mutat. 2020 Jan;41(1):81-102. PMID: 31553106. Viprakasit V et al. Clinical presentation and molecular identification of four uncommon alpha globin variants in Thailand. Acta Haematol. 2014;131(2):88-94. PMID: 24081251. Wong W et al. Thalassemia intermedia due to co-inheritance of beta0/beta(+)-thalassemia and (--SEA) alpha-thalassemia/Hb Westmead (alpha122(H5)His > Gln (alpha2)) in a Chinese family. Hemoglobin. 2004; 28(2):151-6. PMID: 15182058. - |
Heinz body anemia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Nov 29, 2022 | - - |
alpha Thalassemia;C0700299:Heinz body anemia;C3161174:Hemoglobin H disease;C4693823:Erythrocytosis, familial, 7 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 28, 2022 | - - |
Erythrocytosis, familial, 7 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Nov 29, 2022 | - - |
Hemoglobin H disease Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Nov 29, 2022 | - - |
HEMOGLOBIN WESTMEAD Other:1
other, no assertion criteria provided | literature only | OMIM | May 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at