rs2071351

Positions:

• chr6-33076153-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002121.6(HLA-DPB1):​c.100+12A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 1,571,896 control chromosomes in the GnomAD database, including 47,468 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 0.29 (8851 hom., cov: 32)
  • Exomes 𝑓: 0.21 (38617 hom.)
• Consequence: HLA-DPB1 NM_002121.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377

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]

HLA-DPA1 (HGNC:4938): (major histocompatibility complex, class II, DP alpha 1) HLA-DPA1 belongs to the HLA class II alpha chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DPA) and a beta (DPB) chain, 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 and its gene contains 5 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and 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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLA-DPB1	NM_002121.6	c.100+12A>G		intron_variant		ENST00000418931.7
HLA-DPA1	NM_001242525.2	c.-23-2560T>C		intron_variant
HLA-DPA1	NM_001242524.2	c.-99-2484T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DPB1	ENST00000418931.7	c.100+12A>G		intron_variant			NM_002121.6	P1

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44752 AN: 152004 Hom.: 8829 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.307

GnomAD3 exomes AF: 0.244 AC: 54444 AN: 222744 Hom.: 9563 AF XY: 0.243 AC XY: 29442 AN XY: 121168

Gnomad AFR exome AF: 0.525

Gnomad AMR exome AF: 0.177

Gnomad ASJ exome AF: 0.185

Gnomad EAS exome AF: 0.682

Gnomad SAS exome AF: 0.318

Gnomad FIN exome AF: 0.101

Gnomad NFE exome AF: 0.171

Gnomad OTH exome AF: 0.208

GnomAD4 exome AF: 0.208 AC: 294801 AN: 1419774 Hom.: 38617 Cov.: 24 AF XY: 0.210 AC XY: 148106 AN XY: 706940

Gnomad4 AFR exome AF: 0.536

Gnomad4 AMR exome AF: 0.190

Gnomad4 ASJ exome AF: 0.178

Gnomad4 EAS exome AF: 0.635

Gnomad4 SAS exome AF: 0.318

Gnomad4 FIN exome AF: 0.102

Gnomad4 NFE exome AF: 0.178

Gnomad4 OTH exome AF: 0.238

GnomAD4 genome AF: 0.295 AC: 44815 AN: 152122 Hom.: 8851 Cov.: 32 AF XY: 0.292 AC XY: 21714 AN XY: 74392

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.314

Alfa AF: 0.199 Hom.: 2404

Bravo AF: 0.314

Asia WGS AF: 0.456 AC: 1583 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	7.3
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs2071351; hg19: chr6-33043930; COSMIC: COSV69602537; COSMIC: COSV69602537;