rs3117034

chr6-33119581-T-Achr6-33119581-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_001435.2(HLA-DPB2):n.364+2361T>A variant causes a intron, non coding transcript 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 NR_001435.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
HLA-DPB2	NR_001435.2	n.364+2361T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DPB2	ENST00000470997.1	n.364+2361T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.355

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117034; hg19: chr6-33087358;