rs2213568

Variant names:

• chr6-32743799-A-C
• rs2213568
• NM_020056.5:c.83-1360A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-32743799-A-C
• chr6-32743799-A-G
• chr6-32743799-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020056.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DQA2	NM_020056.5	MANE Select	c.83-1360A>C		intron	N/A	NP_064440.1	P01906

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DQA2	ENST00000374940.4	TSL:6 MANE Select	c.83-1360A>C		intron	N/A	ENSP00000364076.3	P01906

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92790 AN: 151796 Hom.: 28684 Cov.: 31

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

African (AFR) AF: 0.638 AC: 26442 AN: 41414

American (AMR) AF: 0.683 AC: 10445 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2228 AN: 3470

East Asian (EAS) AF: 0.709 AC: 3665 AN: 5172

South Asian (SAS) AF: 0.684 AC: 3287 AN: 4808

European-Finnish (FIN) AF: 0.582 AC: 6144 AN: 10550

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38395 AN: 67898

Other (OTH) AF: 0.671 AC: 1417 AN: 2112

Alfa AF: 0.593 Hom.: 65354

Bravo AF: 0.624

Asia WGS AF: 0.689 AC: 2393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.50
DANN	Benign	0.49
PhyloP100		-0.37
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2213568; hg19: chr6-32711576;