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GeneBe

6-32743799-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020056.5(HLA-DQA2):​c.83-1360A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,914 control chromosomes in the GnomAD database, including 28,722 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 0.61 ( 28722 hom., cov: 31)

Consequence

HLA-DQA2
NM_020056.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.373
Variant links:
Genes affected
HLA-DQA2 (HGNC:4943): (major histocompatibility complex, class II, DQ alpha 2) This gene belongs to the HLA class II alpha chain family. The encoded protein forms a heterodimer with a class II beta chain. It is located in intracellular vesicles and plays a central role in the peptide loading of MHC class II molecules by helping to release the CLIP molecule from the peptide binding site. Class II molecules are expressed in antigen presenting cells (B lymphocytes, dendritic cells, macrophages) and are used to present antigenic peptides on the cell surface to be recognized by CD4 T-cells. [provided by RefSeq, Jun 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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HLA-DQA2NM_020056.5 linkuse as main transcriptc.83-1360A>C intron_variant ENST00000374940.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HLA-DQA2ENST00000374940.4 linkuse as main transcriptc.83-1360A>C intron_variant NM_020056.5 P1

Frequencies

GnomAD3 genomes
AF:
0.611
AC:
92790
AN:
151796
Hom.:
28684
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.638
Gnomad AMI
AF:
0.732
Gnomad AMR
AF:
0.683
Gnomad ASJ
AF:
0.642
Gnomad EAS
AF:
0.709
Gnomad SAS
AF:
0.684
Gnomad FIN
AF:
0.582
Gnomad MID
AF:
0.666
Gnomad NFE
AF:
0.566
Gnomad OTH
AF:
0.666
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.611
AC:
92886
AN:
151914
Hom.:
28722
Cov.:
31
AF XY:
0.616
AC XY:
45743
AN XY:
74240
show subpopulations
Gnomad4 AFR
AF:
0.638
Gnomad4 AMR
AF:
0.683
Gnomad4 ASJ
AF:
0.642
Gnomad4 EAS
AF:
0.709
Gnomad4 SAS
AF:
0.684
Gnomad4 FIN
AF:
0.582
Gnomad4 NFE
AF:
0.565
Gnomad4 OTH
AF:
0.671
Alfa
AF:
0.583
Hom.:
34942
Bravo
AF:
0.624
Asia WGS
AF:
0.689
AC:
2393
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.50
DANN
Benign
0.49

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2213568; hg19: chr6-32711576; API