chr6-32638944-G-T

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

2

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

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 HGVSp Effect Exon rank MANE Protein UniProt
HLA-DQA1NM_002122.5 linkc.82+1404G>T intron_variant Intron 1 of 4 ENST00000343139.11 NP_002113.2 P01909A0A173ADG5Q8MH44
HLA-DQA1XM_006715079.5 linkc.82+1404G>T intron_variant Intron 1 of 3 XP_006715142.1
HLA-DQA1-AS1XR_007059544.1 linkn.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-DQA1ENST00000343139.11 linkc.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.:
18
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.:
0
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.:
18
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.

Other links and lift over

dbSNP: rs75983419; hg19: chr6-32606721; API