rs2071550

Variant names:

• chr6-32763163-C-A
• rs2071550
• NM_001300790.2:c.97+211G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-32763163-C-A
• chr6-32763163-C-G
• chr6-32763163-C-T

Variant summary

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

The NM_001300790.2(HLA-DQB2):​c.97+211G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,096 control chromosomes in the GnomAD database, including 7,501 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 0.30 (7501 hom., cov: 32)
• Consequence: HLA-DQB2 NM_001300790.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 33 publications found

Genes affected

HLA-DQB2 (HGNC:4945): (major histocompatibility complex, class II, DQ beta 2) HLA-DQB2 belongs to the family of HLA class II beta chain paralogs. Class II molecules are heterodimers consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. They play 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). Polymorphisms in the alpha and beta chains specify the peptide binding specificity, and typing for these polymorphisms is routinely done for bone marrow transplantation. However this gene, HLA-DQB2, is not routinely typed, as it is not thought to have an effect on transplantation. There is conflicting evidence in the literature and public sequence databases for the protein-coding capacity of HLA-DQB2. Because there is evidence of transcription and an intact ORF, HLA-DQB2 is represented in Entrez Gene and in RefSeq as a protein-coding locus. [provided by RefSeq, Oct 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DQB2	NM_001300790.2	c.97+211G>T		intron_variant	Intron 1 of 5	ENST00000437316.7	NP_001287719.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DQB2	ENST00000437316.7	c.97+211G>T		intron_variant	Intron 1 of 5	6	NM_001300790.2	ENSP00000396330.2
HLA-DQB2	ENST00000435145.6	c.97+211G>T		intron_variant	Intron 1 of 4	6		ENSP00000410512.2
HLA-DQB2	ENST00000411527.5	c.97+211G>T		intron_variant	Intron 1 of 4	6		ENSP00000390431.1
HLA-DQB2	ENST00000427449.1	c.91+211G>T		intron_variant	Intron 1 of 3	6		ENSP00000415997.1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45549 AN: 151978 Hom.: 7503 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.300 AC: 45576 AN: 152096 Hom.: 7501 Cov.: 32 AF XY: 0.308 AC XY: 22901 AN XY: 74348

African (AFR) AF: 0.182 AC: 7538 AN: 41490

American (AMR) AF: 0.345 AC: 5268 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3470

East Asian (EAS) AF: 0.414 AC: 2145 AN: 5178

South Asian (SAS) AF: 0.345 AC: 1664 AN: 4818

European-Finnish (FIN) AF: 0.476 AC: 5032 AN: 10570

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21697 AN: 67988

Other (OTH) AF: 0.284 AC: 600 AN: 2110

Alfa AF: 0.308 Hom.: 30039

Bravo AF: 0.286

Asia WGS AF: 0.373 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.14
DANN	Benign	0.31
PhyloP100		-2.0
PromoterAI		-0.0071	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2071550; hg19: chr6-32730940;