Variant 6-32756412-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001300790.2(HLA-DQB2):c.*41G>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 0.0706 in 1,238,654 control chromosomes in the GnomAD database, including 4,754 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 0.12 ( 1650 hom., cov: 31)

Exomes 𝑓: 0.064 ( 3104 hom. )

Consequence

HLA-DQB2
NM_001300790.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0630

Variant links:

Genes affected

HLA-DQB2 (HGNC:4945): (major histocompatibility complex, class II, DQ beta 2) HLA-DQB2 belongs to the family of HLA class II beta chain paralogs. Class II molecules are heterodimers consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. They play 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). Polymorphisms in the alpha and beta chains specify the peptide binding specificity, and typing for these polymorphisms is routinely done for bone marrow transplantation. However this gene, HLA-DQB2, is not routinely typed, as it is not thought to have an effect on transplantation. There is conflicting evidence in the literature and public sequence databases for the protein-coding capacity of HLA-DQB2. Because there is evidence of transcription and an intact ORF, HLA-DQB2 is represented in Entrez Gene and in RefSeq as a protein-coding locus. [provided by RefSeq, Oct 2010]

HLA-DQB2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
HLA-DQB2	NM_001300790.2 linkuse as main transcript	c.*41G>T	3_prime_UTR_variant	6/6	ENST00000437316.7	NP_001287719.1
HLA-DQB2	NM_001198858.2 linkuse as main transcript	c.*41G>T	3_prime_UTR_variant	5/5		NP_001185787.1
HLA-DQB2	XM_011514560.3 linkuse as main transcript	c.*41G>T	3_prime_UTR_variant	5/5		XP_011512862.1
HLA-DQB2	XM_011514561.4 linkuse as main transcript	c.*41G>T	3_prime_UTR_variant	4/4		XP_011512863.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	Appris	UniProt
HLA-DQB2	ENST00000437316.7 linkuse as main transcript	c.*41G>T	3_prime_UTR_variant	6/6	NM_001300790.2	ENSP00000396330	P1
HLA-DQB2	ENST00000411527.5 linkuse as main transcript	c.*41G>T	3_prime_UTR_variant	5/5		ENSP00000390431		P05538-2
HLA-DQB2	ENST00000427449.1 linkuse as main transcript	c.*41G>T	3_prime_UTR_variant	4/4		ENSP00000415997
HLA-DQB2	ENST00000435145.6 linkuse as main transcript	c.*822G>T	3_prime_UTR_variant	5/5		ENSP00000410512

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17688

AN:

151964

Hom.:

1648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.0461

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.0784

Gnomad EAS

AF:

0.00559

Gnomad SAS

AF:

0.0151

Gnomad FIN

AF:

0.00528

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0675

Gnomad OTH

AF:

0.148

GnomAD3 exomes

AF:

0.0595

AC:

12326

AN:

207218

Hom.:

743

AF XY:

0.0551

AC XY:

6113

AN XY:

110962

show subpopulations

Gnomad AFR exome

AF:

0.239

Gnomad AMR exome

AF:

0.0807

Gnomad ASJ exome

AF:

0.0741

Gnomad EAS exome

AF:

0.00140

Gnomad SAS exome

AF:

0.0192

Gnomad FIN exome

AF:

0.00613

Gnomad NFE exome

AF:

0.0594

Gnomad OTH exome

AF:

0.0806

GnomAD4 exome

AF:

0.0641

AC:

69694

AN:

1086572

Hom.:

3104

Cov.:

AF XY:

0.0615

AC XY:

34010

AN XY:

553426

show subpopulations

Gnomad4 AFR exome

AF:

0.240

Gnomad4 AMR exome

AF:

0.0905

Gnomad4 ASJ exome

AF:

0.0761

Gnomad4 EAS exome

AF:

0.000957

Gnomad4 SAS exome

AF:

0.0191

Gnomad4 FIN exome

AF:

0.00770

Gnomad4 NFE exome

AF:

0.0672

Gnomad4 OTH exome

AF:

0.0736

GnomAD4 genome

AF:

0.116

AC:

17695

AN:

152082

Hom.:

1650

Cov.:

AF XY:

0.112

AC XY:

8330

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.250

Gnomad4 AMR

AF:

0.129

Gnomad4 ASJ

AF:

0.0784

Gnomad4 EAS

AF:

0.00541

Gnomad4 SAS

AF:

0.0151

Gnomad4 FIN

AF:

0.00528

Gnomad4 NFE

AF:

0.0675

Gnomad4 OTH

AF:

0.146

Alfa

AF:

0.0756

Hom.:

578

Bravo

AF:

0.137

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.1

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over