Genetic Variant HLA-DQA1:c.82+1404G>T (chr6-32638944-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002122.5(HLA-DQA1):c.82+1404G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.091 ( 2444 hom., cov: 18)

Exomes 𝑓: 0.076 ( 3754 hom. )

Consequence

HLA-DQA1
NM_002122.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.99

Variant links:

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]

HLA-DQA1 links:

HLA-DQA1-AS1 (HGNC:56667): (HLA-DQA1 antisense RNA 1)

HLA-DQA1-AS1 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 (AMR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
HLA-DQA1	NM_002122.5 link	c.82+1404G>T	intron_variant	Intron 1 of 4	ENST00000343139.11	NP_002113.2	P01909A0A173ADG5Q8MH44
HLA-DQA1	XM_006715079.5 link	c.82+1404G>T	intron_variant	Intron 1 of 3		XP_006715142.1
HLA-DQA1-AS1	XR_007059544.1 link	n.1219C>A	non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DQA1	ENST00000343139.11 link	c.82+1404G>T		intron_variant	Intron 1 of 4	6	NM_002122.5	ENSP00000339398.5		P01909

Frequencies

GnomAD3 genomes

AF:

0.0911

AC:

10270

AN:

112674

Hom.:

2442

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0660

Gnomad AMI

AF:

0.0332

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.00943

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.0769

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.105

GnomAD3 exomes

AF:

0.0585

AC:

5529

AN:

94508

Hom.:

1126

AF XY:

0.0636

AC XY:

3306

AN XY:

51946

show subpopulations

Gnomad AFR exome

AF:

0.0263

Gnomad AMR exome

AF:

0.0359

Gnomad ASJ exome

AF:

0.0942

Gnomad EAS exome

AF:

0.00460

Gnomad SAS exome

AF:

0.0888

Gnomad FIN exome

AF:

0.0915

Gnomad NFE exome

AF:

0.0617

Gnomad OTH exome

AF:

0.0549

GnomAD4 exome

AF:

0.0763

AC:

17742

AN:

232676

Hom.:

3754

Cov.:

AF XY:

0.0792

AC XY:

10584

AN XY:

133562

show subpopulations

Gnomad4 AFR exome

AF:

0.0439

Gnomad4 AMR exome

AF:

0.0476

Gnomad4 ASJ exome

AF:

0.0963

Gnomad4 EAS exome

AF:

0.00754

Gnomad4 SAS exome

AF:

0.0931

Gnomad4 FIN exome

AF:

0.110

Gnomad4 NFE exome

AF:

0.0767

Gnomad4 OTH exome

AF:

0.0748

GnomAD4 genome

AF:

0.0911

AC:

10275

AN:

112792

Hom.:

2444

Cov.:

AF XY:

0.0924

AC XY:

5071

AN XY:

54852

show subpopulations

Gnomad4 AFR

AF:

0.0661

Gnomad4 AMR

AF:

0.112

Gnomad4 ASJ

AF:

0.129

Gnomad4 EAS

AF:

0.00969

Gnomad4 SAS

AF:

0.101

Gnomad4 FIN

AF:

0.122

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.53

DANN

Benign

0.36

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

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