rs7383287

Positions:

• chr6-32815309-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_002120.4(HLA-DOB):​c.96T>C​(p.Asp32=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 1,613,526 control chromosomes in the GnomAD database, including 33,469 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 0.19 (2772 hom., cov: 32)
  • Exomes 𝑓: 0.20 (30697 hom.)
• Consequence: HLA-DOB NM_002120.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

Genes affected

HLA-DOB (HGNC:4937): (major histocompatibility complex, class II, DO beta) HLA-DOB belongs to the HLA class II beta chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DOA) and a beta chain (DOB), both anchored in the membrane. It is located in intracellular vesicles. DO suppresses peptide loading of MHC class II molecules by inhibiting HLA-DM. 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. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BP7: Synonymous conserved (PhyloP=0.046 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLA-DOB	NM_002120.4	c.96T>C	p.Asp32=	synonymous_variant	2/6	ENST00000438763.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DOB	ENST00000438763.7	c.96T>C	p.Asp32=	synonymous_variant	2/6		NM_002120.4	P1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28196 AN: 152034 Hom.: 2773 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0407

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.183

GnomAD3 exomes AF: 0.176 AC: 44098 AN: 251012 Hom.: 4428 AF XY: 0.181 AC XY: 24616 AN XY: 135682

Gnomad AFR exome AF: 0.175

Gnomad AMR exome AF: 0.120

Gnomad ASJ exome AF: 0.225

Gnomad EAS exome AF: 0.0449

Gnomad SAS exome AF: 0.163

Gnomad FIN exome AF: 0.170

Gnomad NFE exome AF: 0.214

Gnomad OTH exome AF: 0.181

GnomAD4 exome AF: 0.200 AC: 292584 AN: 1461374 Hom.: 30697 Cov.: 38 AF XY: 0.201 AC XY: 146455 AN XY: 726902

Gnomad4 AFR exome AF: 0.171

Gnomad4 AMR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.224

Gnomad4 EAS exome AF: 0.0433

Gnomad4 SAS exome AF: 0.164

Gnomad4 FIN exome AF: 0.171

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.192

GnomAD4 genome AF: 0.185 AC: 28193 AN: 152152 Hom.: 2772 Cov.: 32 AF XY: 0.180 AC XY: 13394 AN XY: 74390

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0404

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.180

Alfa AF: 0.206 Hom.: 6820

Bravo AF: 0.181

Asia WGS AF: 0.100 AC: 348 AN: 3478

EpiCase AF: 0.232

EpiControl AF: 0.224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	6.1
DANN	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7383287; hg19: chr6-32783086; COSMIC: COSV71270982;