rs7774954
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001300790.2(HLA-DQB2):c.*41G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0706 in 1,238,654 control chromosomes in the GnomAD database, including 4,754 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 0.12 ( 1650 hom., cov: 31)
Exomes 𝑓: 0.064 ( 3104 hom. )
Consequence
HLA-DQB2
NM_001300790.2 3_prime_UTR
NM_001300790.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0630
Genes affected
HLA-DQB2 (HGNC:4945): (major histocompatibility complex, class II, DQ beta 2) HLA-DQB2 belongs to the family of HLA class II beta chain paralogs. Class II molecules are heterodimers consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. They play 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). Polymorphisms in the alpha and beta chains specify the peptide binding specificity, and typing for these polymorphisms is routinely done for bone marrow transplantation. However this gene, HLA-DQB2, is not routinely typed, as it is not thought to have an effect on transplantation. There is conflicting evidence in the literature and public sequence databases for the protein-coding capacity of HLA-DQB2. Because there is evidence of transcription and an intact ORF, HLA-DQB2 is represented in Entrez Gene and in RefSeq as a protein-coding locus. [provided by RefSeq, Oct 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-DQB2 | NM_001300790.2 | c.*41G>T | 3_prime_UTR_variant | 6/6 | ENST00000437316.7 | ||
HLA-DQB2 | NM_001198858.2 | c.*41G>T | 3_prime_UTR_variant | 5/5 | |||
HLA-DQB2 | XM_011514560.3 | c.*41G>T | 3_prime_UTR_variant | 5/5 | |||
HLA-DQB2 | XM_011514561.4 | c.*41G>T | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-DQB2 | ENST00000437316.7 | c.*41G>T | 3_prime_UTR_variant | 6/6 | NM_001300790.2 | P1 | |||
HLA-DQB2 | ENST00000411527.5 | c.*41G>T | 3_prime_UTR_variant | 5/5 | |||||
HLA-DQB2 | ENST00000427449.1 | c.*41G>T | 3_prime_UTR_variant | 4/4 | |||||
HLA-DQB2 | ENST00000435145.6 | c.*822G>T | 3_prime_UTR_variant | 5/5 |
Frequencies
GnomAD3 genomes ? AF: 0.116 AC: 17688AN: 151964Hom.: 1648 Cov.: 31
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GnomAD3 exomes AF: 0.0595 AC: 12326AN: 207218Hom.: 743 AF XY: 0.0551 AC XY: 6113AN XY: 110962
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GnomAD4 exome AF: 0.0641 AC: 69694AN: 1086572Hom.: 3104 Cov.: 15 AF XY: 0.0615 AC XY: 34010AN XY: 553426
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GnomAD4 genome ? AF: 0.116 AC: 17695AN: 152082Hom.: 1650 Cov.: 31 AF XY: 0.112 AC XY: 8330AN XY: 74366
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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