NM_002121.6:c.*1588G>A

Variant names:

• chr6-33088122-G-A
• rs3128965
• NM_002121.6:c.*1588G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002121.6(HLA-DPB1):​c.*1588G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,096 control chromosomes in the GnomAD database, including 1,585 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 0.14 (1585 hom., cov: 32)
• Consequence: HLA-DPB1 NM_002121.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 26 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPB1	NM_002121.6	c.*1588G>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000418931.7	NP_002112.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DPB1	ENST00000418931.7	c.*1588G>A		3_prime_UTR_variant	Exon 6 of 6	6	NM_002121.6	ENSP00000408146.2
HLA-DPB1	ENST00000428835.6	c.*1588G>A		3_prime_UTR_variant	Exon 6 of 6	6		ENSP00000412654.2
HLA-DPB1	ENST00000714457.1	n.*136G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21101 AN: 151978 Hom.: 1586 Cov.: 32

Gnomad AFR AF: 0.0734

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.143

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.139 AC: 21100 AN: 152096 Hom.: 1585 Cov.: 32 AF XY: 0.138 AC XY: 10267 AN XY: 74374

African (AFR) AF: 0.0734 AC: 3045 AN: 41500

American (AMR) AF: 0.150 AC: 2296 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3466

East Asian (EAS) AF: 0.134 AC: 693 AN: 5178

South Asian (SAS) AF: 0.162 AC: 777 AN: 4800

European-Finnish (FIN) AF: 0.166 AC: 1754 AN: 10564

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11739 AN: 67982

Other (OTH) AF: 0.144 AC: 304 AN: 2110

Alfa AF: 0.151 Hom.: 3765

Bravo AF: 0.132

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.75
PhyloP100		1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3128965; hg19: chr6-33055899;