rs78202368

Variant names:

• chr6-32666786-C-G
• rs78202368
• ENST00000399084.5:c.-63-116G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-32666786-C-G
• chr6-32666786-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000399084.5(HLA-DQB1):​c.-63-116G>C 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: not found (cov: 8)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HLA-DQB1 ENST00000399084.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 8 publications found

Genes affected

HLA-DQB1 (HGNC:4944): (major histocompatibility complex, class II, DQ beta 1) HLA-DQB1 belongs to the HLA class II beta chain paralogs. This 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 beta chain is approximately 26-28 kDa and it contains six exons. Exon 1 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 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. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399084.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DQB1	NM_002123.5	MANE Select	c.-179G>C		upstream_gene	N/A	NP_002114.3
	HLA-DQB1	NM_001243961.2		c.-179G>C		upstream_gene	N/A	NP_001230890.1	Q5SU54

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DQB1	ENST00000399084.5	TSL:6	c.-63-116G>C		intron	N/A	ENSP00000382034.1
	HLA-DQB1	ENST00000434651.7	TSL:6 MANE Select	c.-179G>C		upstream_gene	N/A	ENSP00000407332.2
	HLA-DQB1	ENST00000374943.8	TSL:6	c.-179G>C		upstream_gene	N/A	ENSP00000364080.4	Q5SU54

Frequencies

GnomAD3 genomes Cov.: 8

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 144742 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 76478

African (AFR) AF: 0.00 AC: 0 AN: 3820

American (AMR) AF: 0.00 AC: 0 AN: 3144

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3598

East Asian (EAS) AF: 0.00 AC: 0 AN: 8802

South Asian (SAS) AF: 0.00 AC: 0 AN: 12196

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 13712

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 724

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 90258

Other (OTH) AF: 0.00 AC: 0 AN: 8488

GnomAD4 genome Cov.: 8

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.7
DANN	Benign	0.61
PhyloP100		-2.1
PromoterAI		-0.21	Neutral

Splicing

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

Other links and lift over

dbSNP: rs78202368; hg19: chr6-32634563;