rs3117016

Variant names:

• chr6-33127739-G-A
• rs3117016
• ENST00000470997.1:n.365-79G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-33127739-G-A
• chr6-33127739-G-C
• chr6-33127739-G-T

Variant summary

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

The ENST00000470997.1(HLA-DPB2):​n.365-79G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 614,684 control chromosomes in the GnomAD database, including 44,196 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 0.34 (9461 hom., cov: 31)
  • Exomes 𝑓: 0.38 (34735 hom.)
• Consequence: HLA-DPB2 ENST00000470997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 38 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.365-79G>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.365-79G>A		intron_variant	Intron 2 of 4	6
ENSG00000291111	ENST00000782892.1	n.429+10519G>A		intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782893.1	n.403+10519G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52284 AN: 151806 Hom.: 9464 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.358

GnomAD4 exome AF: 0.380 AC: 175855 AN: 462760 Hom.: 34735 AF XY: 0.383 AC XY: 93882 AN XY: 244990

African (AFR) AF: 0.227 AC: 2905 AN: 12810

American (AMR) AF: 0.271 AC: 5746 AN: 21196

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 7136 AN: 13464

East Asian (EAS) AF: 0.434 AC: 13380 AN: 30812

South Asian (SAS) AF: 0.428 AC: 20476 AN: 47810

European-Finnish (FIN) AF: 0.347 AC: 14546 AN: 41940

Middle Eastern (MID) AF: 0.419 AC: 1311 AN: 3130

European-Non Finnish (NFE) AF: 0.378 AC: 100618 AN: 265872

Other (OTH) AF: 0.378 AC: 9737 AN: 25726

GnomAD4 genome AF: 0.344 AC: 52285 AN: 151924 Hom.: 9461 Cov.: 31 AF XY: 0.344 AC XY: 25540 AN XY: 74272

African (AFR) AF: 0.239 AC: 9911 AN: 41412

American (AMR) AF: 0.329 AC: 5011 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1873 AN: 3472

East Asian (EAS) AF: 0.437 AC: 2264 AN: 5176

South Asian (SAS) AF: 0.446 AC: 2150 AN: 4818

European-Finnish (FIN) AF: 0.363 AC: 3833 AN: 10548

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26159 AN: 67924

Other (OTH) AF: 0.356 AC: 752 AN: 2114

Alfa AF: 0.377 Hom.: 48992

Bravo AF: 0.336

Asia WGS AF: 0.434 AC: 1512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.1
DANN	Benign	0.70
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs3117016; hg19: chr6-33095516;