rs9273012

chr6-32643864-A-G

Variant summary

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

The XM_006715079.5(HLA-DQA1):c.613+1611A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 150,892 control chromosomes in the GnomAD database, including 6,798 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 0.29 (6798 hom., cov: 27)
  • Exomes 𝑓: 0.033 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HLA-DQA1 XM_006715079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

HLA-DQA1 (HGNC:4942): (major histocompatibility complex, class II, DQ alpha 1) HLA-DQA1 belongs to the HLA class II alpha chain paralogues. The class II molecule is a heterodimer consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B Lymphocytes, dendritic cells, macrophages). The alpha chain is approximately 33-35 kDa. It is encoded by 5 exons; exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, and exon 4 encodes the transmembrane domain and the cytoplasmic tail. Within the DQ molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to four different molecules. Typing for these polymorphisms is routinely done for bone marrow transplantation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLA-DQA1	XM_006715079.5	c.613+1611A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DQA1	ENST00000460633.1	n.2252A>G		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.291 AC: 43934 AN: 150774 Hom.: 6796 Cov.: 27

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.310

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0326 AC: 3 AN: 92 Hom.: 0 Cov.: 0 AF XY: 0.0484 AC XY: 3 AN XY: 62

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.0349

GnomAD4 genome AF: 0.291 AC: 43959 AN: 150892 Hom.: 6798 Cov.: 27 AF XY: 0.291 AC XY: 21395 AN XY: 73642

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.308

Alfa AF: 0.305 Hom.: 5895

Bravo AF: 0.297

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.5
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9273012; hg19: chr6-32611641;