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rs2187668

Variant summary

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

The NM_002122.5(HLA-DQA1):c.82+567C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 127,560 control chromosomes in the GnomAD database, including 8 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 0.0033 ( 8 hom., cov: 20)

Consequence

HLA-DQA1
NM_002122.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0980
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]

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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=-0.85).
BS2
High Homozygotes in GnomAd at 9 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HLA-DQA1NM_002122.5 linkuse as main transcriptc.82+567C>T intron_variant ENST00000343139.11
HLA-DQA1-AS1XR_007059544.1 linkuse as main transcriptn.2056G>A non_coding_transcript_exon_variant 2/2
HLA-DQA1XM_006715079.5 linkuse as main transcriptc.82+567C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HLA-DQA1ENST00000343139.11 linkuse as main transcriptc.82+567C>T intron_variant NM_002122.5 P1

Frequencies

GnomAD3 genomes
AF:
0.00335
AC:
427
AN:
127434
Hom.:
9
Cov.:
20
show subpopulations
Gnomad AFR
AF:
0.00113
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00247
Gnomad ASJ
AF:
0.00256
Gnomad EAS
AF:
0.00459
Gnomad SAS
AF:
0.00474
Gnomad FIN
AF:
0.00135
Gnomad MID
AF:
0.0165
Gnomad NFE
AF:
0.00492
Gnomad OTH
AF:
0.00646
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00335
AC:
427
AN:
127560
Hom.:
8
Cov.:
20
AF XY:
0.00357
AC XY:
222
AN XY:
62154
show subpopulations
Gnomad4 AFR
AF:
0.00119
Gnomad4 AMR
AF:
0.00239
Gnomad4 ASJ
AF:
0.00256
Gnomad4 EAS
AF:
0.00481
Gnomad4 SAS
AF:
0.00422
Gnomad4 FIN
AF:
0.00135
Gnomad4 NFE
AF:
0.00492
Gnomad4 OTH
AF:
0.00639
Alfa
AF:
0.116
Hom.:
1884
Asia WGS
AF:
0.0670
AC:
233
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
4.1
Dann
Benign
0.33

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.

Other links and lift over

dbSNP: rs2187668; hg19: chr6-32605884; API