Variant rs9272535 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_002122.5(HLA-DQA1):c.82+1439G>A 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 0.0017 ( 2 hom., cov: 18)

Exomes 𝑓: 0.0033 ( 94 hom. )

Consequence

HLA-DQA1
NM_002122.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.236

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:):

HLA-DQA1-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
HLA-DQA1	NM_002122.5 linkuse as main transcript	c.82+1439G>A	intron_variant		ENST00000343139.11
HLA-DQA1-AS1	XR_007059544.1 linkuse as main transcript	n.1184C>T	non_coding_transcript_exon_variant	2/2
HLA-DQA1	XM_006715079.5 linkuse as main transcript	c.82+1439G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DQA1	ENST00000343139.11 linkuse as main transcript	c.82+1439G>A		intron_variant			NM_002122.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00166

AC:

192

AN:

115648

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00235

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00195

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00285

Gnomad SAS

AF:

0.00258

Gnomad FIN

AF:

0.00360

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000847

Gnomad OTH

AF:

0.00199

GnomAD3 exomes

AF:

0.0000299

AC:

AN:

100358

Hom.:

AF XY:

0.0000360

AC XY:

AN XY:

55500

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000784

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00328

AC:

756

AN:

230626

Hom.:

Cov.:

AF XY:

0.00360

AC XY:

477

AN XY:

132640

show subpopulations

Gnomad4 AFR exome

AF:

0.00497

Gnomad4 AMR exome

AF:

0.00723

Gnomad4 ASJ exome

AF:

0.000732

Gnomad4 EAS exome

AF:

0.00353

Gnomad4 SAS exome

AF:

0.000960

Gnomad4 FIN exome

AF:

0.00518

Gnomad4 NFE exome

AF:

0.00328

Gnomad4 OTH exome

AF:

0.00523

GnomAD4 genome

AF:

0.00166

AC:

192

AN:

115760

Hom.:

Cov.:

AF XY:

0.00174

AC XY:

AN XY:

56346

show subpopulations

Gnomad4 AFR

AF:

0.00234

Gnomad4 AMR

AF:

0.00195

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00286

Gnomad4 SAS

AF:

0.00257

Gnomad4 FIN

AF:

0.00360

Gnomad4 NFE

AF:

0.000847

Gnomad4 OTH

AF:

0.00196

Alfa

AF:

0.210

Hom.:

771

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.9

DANN

Benign

0.86

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