rs1048381
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_002122.5(HLA-DQA1):c.672G>A(p.Gly224=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0202 in 1,220,146 control chromosomes in the GnomAD database, including 4,156 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0071 ( 4 hom., cov: 16)
Exomes 𝑓: 0.021 ( 4152 hom. )
Consequence
HLA-DQA1
NM_002122.5 synonymous
NM_002122.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.610
Genes affected
HLA-DQA1 (HGNC:4942): (major histocompatibility complex, class II, DQ alpha 1) HLA-DQA1 belongs to the HLA class II alpha chain paralogues. The class II molecule is a heterodimer consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B Lymphocytes, dendritic cells, macrophages). The alpha chain is approximately 33-35 kDa. It is encoded by 5 exons; exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, and exon 4 encodes the transmembrane domain and the cytoplasmic tail. Within the DQ molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to four different molecules. Typing for these polymorphisms is routinely done for bone marrow transplantation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP7
Synonymous conserved (PhyloP=-0.61 with no splicing effect.
BA1
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HLA-DQA1 | NM_002122.5 | c.672G>A | p.Gly224= | synonymous_variant | 4/5 | ENST00000343139.11 | NP_002113.2 | |
HLA-DQA1 | XM_006715079.5 | c.613+415G>A | intron_variant | XP_006715142.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HLA-DQA1 | ENST00000343139.11 | c.672G>A | p.Gly224= | synonymous_variant | 4/5 | NM_002122.5 | ENSP00000339398 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00713 AC: 748AN: 104924Hom.: 4 Cov.: 16
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GnomAD3 exomes AF: 0.130 AC: 29319AN: 225234Hom.: 4110 AF XY: 0.126 AC XY: 15383AN XY: 122494
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GnomAD4 exome AF: 0.0214 AC: 23906AN: 1115114Hom.: 4152 Cov.: 32 AF XY: 0.0217 AC XY: 12148AN XY: 560146
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GnomAD4 genome AF: 0.00713 AC: 749AN: 105032Hom.: 4 Cov.: 16 AF XY: 0.00742 AC XY: 377AN XY: 50790
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at