rs9276440

Variant names:

• chr6-32747006-A-G
• rs9276440
• NM_020056.5:c.*445A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-32747006-A-G
• chr6-32747006-A-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_020056.5(HLA-DQA2):​c.*445A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 257,410 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00024 (0 hom., cov: 29)
  • Exomes 𝑓: 0.000038 (0 hom.)
• Consequence: HLA-DQA2 NM_020056.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 14 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DQA2	NM_020056.5	c.*445A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000374940.4	NP_064440.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DQA2	ENST00000374940.4	c.*445A>G		3_prime_UTR_variant	Exon 5 of 5	6	NM_020056.5	ENSP00000364076.3

Frequencies

GnomAD3 genomes AF: 0.000244 AC: 37 AN: 151692 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.000873

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000656

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000379 AC: 4 AN: 105598 Hom.: 0 Cov.: 0 AF XY: 0.0000359 AC XY: 2 AN XY: 55740

African (AFR) AF: 0.000874 AC: 3 AN: 3432

American (AMR) AF: 0.00 AC: 0 AN: 5666

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2392

East Asian (EAS) AF: 0.00 AC: 0 AN: 5732

South Asian (SAS) AF: 0.00 AC: 0 AN: 14982

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4186

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 374

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 63306

Other (OTH) AF: 0.000181 AC: 1 AN: 5528

GnomAD4 genome AF: 0.000244 AC: 37 AN: 151812 Hom.: 0 Cov.: 29 AF XY: 0.000283 AC XY: 21 AN XY: 74194

African (AFR) AF: 0.000870 AC: 36 AN: 41360

American (AMR) AF: 0.0000655 AC: 1 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.00 AC: 0 AN: 4814

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10502

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67934

Other (OTH) AF: 0.00 AC: 0 AN: 2106

Alfa AF: 0.00 Hom.: 1164

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		0.019

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: rs9276440; hg19: chr6-32714783;