NM_020056.5:c.*563C>T

Variant names:

• chr6-32747124-C-T
• rs9276442
• NM_020056.5:c.*563C>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.*563C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 157,292 control chromosomes in the GnomAD database, including 1,607 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 0.11 (1588 hom., cov: 27)
  • Exomes 𝑓: 0.046 (19 hom.)
• Consequence: HLA-DQA2 NM_020056.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DQA2	NM_020056.5	MANE Select	c.*563C>T		3_prime_UTR	Exon 5 of 5	NP_064440.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DQA2	ENST00000374940.4	TSL:6 MANE Select	c.*563C>T		3_prime_UTR	Exon 5 of 5	ENSP00000364076.3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17080 AN: 149116 Hom.: 1586 Cov.: 27

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0774

Gnomad EAS AF: 0.00566

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.00505

Gnomad MID AF: 0.0353

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.0463 AC: 374 AN: 8076 Hom.: 19 Cov.: 0 AF XY: 0.0430 AC XY: 187 AN XY: 4352

African (AFR) AF: 0.135 AC: 10 AN: 74

American (AMR) AF: 0.0801 AC: 133 AN: 1660

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 2 AN: 62

East Asian (EAS) AF: 0.00 AC: 0 AN: 426

South Asian (SAS) AF: 0.0130 AC: 11 AN: 846

European-Finnish (FIN) AF: 0.00862 AC: 1 AN: 116

Middle Eastern (MID) AF: 0.0625 AC: 1 AN: 16

European-Non Finnish (NFE) AF: 0.0419 AC: 191 AN: 4558

Other (OTH) AF: 0.0786 AC: 25 AN: 318

GnomAD4 genome AF: 0.115 AC: 17088 AN: 149216 Hom.: 1588 Cov.: 27 AF XY: 0.110 AC XY: 8016 AN XY: 72696

African (AFR) AF: 0.248 AC: 9878 AN: 39884

American (AMR) AF: 0.128 AC: 1912 AN: 14920

Ashkenazi Jewish (ASJ) AF: 0.0774 AC: 267 AN: 3450

East Asian (EAS) AF: 0.00548 AC: 28 AN: 5110

South Asian (SAS) AF: 0.0137 AC: 65 AN: 4754

European-Finnish (FIN) AF: 0.00505 AC: 51 AN: 10094

Middle Eastern (MID) AF: 0.0345 AC: 10 AN: 290

European-Non Finnish (NFE) AF: 0.0670 AC: 4539 AN: 67738

Other (OTH) AF: 0.143 AC: 296 AN: 2066

Alfa AF: 0.0908 Hom.: 336

Bravo AF: 0.137

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.64
PhyloP100		0.60
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs9276442; hg19: chr6-32714901;