6-32664858-A-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002123.5(HLA-DQB1):āc.319T>Cā(p.Leu107Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000184 in 1,067,978 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00027 ( 3 hom., cov: 18)
Exomes š: 0.00017 ( 19 hom. )
Consequence
HLA-DQB1
NM_002123.5 synonymous
NM_002123.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.69
Genes affected
HLA-DQB1 (HGNC:4944): (major histocompatibility complex, class II, DQ beta 1) HLA-DQB1 belongs to the HLA class II beta chain paralogs. This 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 beta chain is approximately 26-28 kDa and it contains six exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and exon 5 encodes 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. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 6-32664858-A-G is Benign according to our data. Variant chr6-32664858-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2656472.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.69 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HLA-DQB1 | ENST00000434651.7 | c.319T>C | p.Leu107Leu | synonymous_variant | Exon 2 of 5 | 6 | NM_002123.5 | ENSP00000407332.2 | ||
HLA-DQB1 | ENST00000374943.8 | c.319T>C | p.Leu107Leu | synonymous_variant | Exon 2 of 6 | 6 | ENSP00000364080.4 |
Frequencies
GnomAD3 genomes AF: 0.000272 AC: 32AN: 117568Hom.: 3 Cov.: 18
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GnomAD3 exomes AF: 0.000244 AC: 35AN: 143434Hom.: 6 AF XY: 0.000252 AC XY: 20AN XY: 79446
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GnomAD4 exome AF: 0.000174 AC: 165AN: 950336Hom.: 19 Cov.: 25 AF XY: 0.000170 AC XY: 82AN XY: 483526
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GnomAD4 genome AF: 0.000272 AC: 32AN: 117642Hom.: 3 Cov.: 18 AF XY: 0.000263 AC XY: 15AN XY: 57014
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jul 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
HLA-DQB1: BP4, BP7 -
Computational 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