rs9276429

Positions:

• chr6-32744327-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020056.5(HLA-DQA2):​c.83-832G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 148,222 control chromosomes in the GnomAD database, including 30,058 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 (30058 hom., cov: 31)
• Consequence: HLA-DQA2 NM_020056.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-DQA2	NM_020056.5	c.83-832G>A		intron_variant		ENST00000374940.4	NP_064440.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DQA2	ENST00000374940.4	c.83-832G>A		intron_variant		6	NM_020056.5	ENSP00000364076.3

Frequencies

GnomAD3 genomes AF: 0.639 AC: 94700 AN: 148106 Hom.: 30018 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.694

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.640 AC: 94796 AN: 148222 Hom.: 30058 Cov.: 31 AF XY: 0.646 AC XY: 46832 AN XY: 72532

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.698

Alfa AF: 0.634 Hom.: 5997

Asia WGS AF: 0.795 AC: 2760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.74

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

Other links and lift over

dbSNP: rs9276429; hg19: chr6-32712104;