Menu
GeneBe

rs9277535

Variant summary

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

The NM_002121.6(HLA-DPB1):c.*550A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 161,136 control chromosomes in the GnomAD database, including 5,260 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 0.25 ( 5239 hom., cov: 32)
Exomes 𝑓: 0.033 ( 21 hom. )

Consequence

HLA-DPB1
NM_002121.6 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.133
Variant links:
Genes affected
HLA-DPB1 (HGNC:4940): (major histocompatibility complex, class II, DP beta 1) HLA-DPB belongs to the HLA class II beta chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DPA) and a beta chain (DPB), 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 beta chain is approximately 26-28 kDa and its gene contains 6 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and exon 5 encodes the cytoplasmic tail. Within the DP molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to 4 different molecules. [provided by RefSeq, Jul 2008]

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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HLA-DPB1NM_002121.6 linkuse as main transcriptc.*550A>G 3_prime_UTR_variant 6/6 ENST00000418931.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HLA-DPB1ENST00000418931.7 linkuse as main transcriptc.*550A>G 3_prime_UTR_variant 6/6 NM_002121.6 P1
HLA-DPB1ENST00000416804.1 linkuse as main transcriptc.*537A>G 3_prime_UTR_variant 5/5

Frequencies

GnomAD3 genomes
AF:
0.252
AC:
38313
AN:
152078
Hom.:
5226
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.243
Gnomad AMI
AF:
0.103
Gnomad AMR
AF:
0.235
Gnomad ASJ
AF:
0.173
Gnomad EAS
AF:
0.624
Gnomad SAS
AF:
0.268
Gnomad FIN
AF:
0.201
Gnomad MID
AF:
0.232
Gnomad NFE
AF:
0.245
Gnomad OTH
AF:
0.272
GnomAD4 exome
AF:
0.0329
AC:
294
AN:
8940
Hom.:
21
Cov.:
0
AF XY:
0.0345
AC XY:
154
AN XY:
4468
show subpopulations
Gnomad4 AFR exome
AF:
0.139
Gnomad4 AMR exome
AF:
0.0129
Gnomad4 ASJ exome
AF:
0.00952
Gnomad4 EAS exome
AF:
0.260
Gnomad4 SAS exome
AF:
0.00643
Gnomad4 FIN exome
AF:
0.0427
Gnomad4 NFE exome
AF:
0.0306
Gnomad4 OTH exome
AF:
0.0377
GnomAD4 genome
AF:
0.252
AC:
38341
AN:
152196
Hom.:
5239
Cov.:
32
AF XY:
0.249
AC XY:
18525
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.243
Gnomad4 AMR
AF:
0.235
Gnomad4 ASJ
AF:
0.173
Gnomad4 EAS
AF:
0.624
Gnomad4 SAS
AF:
0.266
Gnomad4 FIN
AF:
0.201
Gnomad4 NFE
AF:
0.245
Gnomad4 OTH
AF:
0.282
Alfa
AF:
0.250
Hom.:
6309
Bravo
AF:
0.253
Asia WGS
AF:
0.396
AC:
1374
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
2.3
Dann
Benign
0.78

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: rs9277535; hg19: chr6-33054861; API