rs3117034

Variant names:

• chr6-33119581-T-A
• rs3117034
• ENST00000470997.1:n.364+2361T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-33119581-T-A
• chr6-33119581-T-C

Variant summary

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

The ENST00000470997.1(HLA-DPB2):​n.364+2361T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,202 control chromosomes in the GnomAD database, including 10,268 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 0.35 (10268 hom., cov: 33)
• Consequence: HLA-DPB2 ENST00000470997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 15 publications found

Genes affected

HLA-DPB2 (HGNC:4941): (major histocompatibility complex, class II, DP beta 2 (pseudogene))

ENSG00000291111 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.364+2361T>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DPB2	ENST00000470997.1	n.364+2361T>A		intron_variant	Intron 2 of 4	6
ENSG00000291111	ENST00000782892.1	n.429+2361T>A		intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782893.1	n.403+2361T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53263 AN: 152084 Hom.: 10269 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.350 AC: 53274 AN: 152202 Hom.: 10268 Cov.: 33 AF XY: 0.353 AC XY: 26240 AN XY: 74420

African (AFR) AF: 0.200 AC: 8291 AN: 41542

American (AMR) AF: 0.289 AC: 4416 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1980 AN: 3466

East Asian (EAS) AF: 0.374 AC: 1937 AN: 5178

South Asian (SAS) AF: 0.551 AC: 2656 AN: 4824

European-Finnish (FIN) AF: 0.406 AC: 4297 AN: 10588

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28412 AN: 67988

Other (OTH) AF: 0.355 AC: 751 AN: 2116

Alfa AF: 0.387 Hom.: 1579

Bravo AF: 0.329

Asia WGS AF: 0.446 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.43
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs3117034; hg19: chr6-33087358;