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GeneBe

6-32744470-T-C

Variant summary

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

The NM_020056.5(HLA-DQA2):​c.83-689T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 150,658 control chromosomes in the GnomAD database, including 29,191 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 0.62 ( 29191 hom., cov: 30)

Consequence

HLA-DQA2
NM_020056.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.709
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HLA-DQA2NM_020056.5 linkuse as main transcriptc.83-689T>C intron_variant ENST00000374940.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HLA-DQA2ENST00000374940.4 linkuse as main transcriptc.83-689T>C intron_variant NM_020056.5 P1

Frequencies

GnomAD3 genomes
AF:
0.620
AC:
93338
AN:
150538
Hom.:
29149
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.637
Gnomad AMI
AF:
0.732
Gnomad AMR
AF:
0.684
Gnomad ASJ
AF:
0.669
Gnomad EAS
AF:
0.846
Gnomad SAS
AF:
0.791
Gnomad FIN
AF:
0.576
Gnomad MID
AF:
0.683
Gnomad NFE
AF:
0.567
Gnomad OTH
AF:
0.678
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.620
AC:
93437
AN:
150658
Hom.:
29191
Cov.:
30
AF XY:
0.626
AC XY:
46124
AN XY:
73626
show subpopulations
Gnomad4 AFR
AF:
0.637
Gnomad4 AMR
AF:
0.685
Gnomad4 ASJ
AF:
0.669
Gnomad4 EAS
AF:
0.845
Gnomad4 SAS
AF:
0.792
Gnomad4 FIN
AF:
0.576
Gnomad4 NFE
AF:
0.567
Gnomad4 OTH
AF:
0.683
Alfa
AF:
0.596
Hom.:
27300
Bravo
AF:
0.635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.64
DANN
Benign
0.56

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: rs9276431; hg19: chr6-32712247; API