rs7768538
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001300790.2(HLA-DQB2):c.98-118G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 1,340,726 control chromosomes in the GnomAD database, including 236,528 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 0.64 ( 31622 hom., cov: 32)
Exomes 𝑓: 0.58 ( 204906 hom. )
Consequence
HLA-DQB2
NM_001300790.2 intron
NM_001300790.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0150
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-DQB2 | NM_001300790.2 | c.98-118G>T | intron_variant | ENST00000437316.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-DQB2 | ENST00000437316.7 | c.98-118G>T | intron_variant | NM_001300790.2 | P1 | ||||
HLA-DQB2 | ENST00000411527.5 | c.98-118G>T | intron_variant | ||||||
HLA-DQB2 | ENST00000427449.1 | c.94-118G>T | intron_variant | ||||||
HLA-DQB2 | ENST00000435145.6 | c.98-118G>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.639 AC: 96995AN: 151858Hom.: 31575 Cov.: 32
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GnomAD4 exome AF: 0.578 AC: 687502AN: 1188750Hom.: 204906 AF XY: 0.586 AC XY: 345394AN XY: 589200
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GnomAD4 genome ? AF: 0.639 AC: 97103AN: 151976Hom.: 31622 Cov.: 32 AF XY: 0.646 AC XY: 48013AN XY: 74290
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ClinVar
Not reported inComputational scores
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Name
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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