6-33115344-T-C

Position:

• chr6-33115344-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.101-1613T>C 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 0.264 in 151,942 control chromosomes in the GnomAD database, including 5,690 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 0.26 (5690 hom., cov: 31)
• Consequence: HLA-DPB2 NR_001435.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602

Genes affected

(HGNC:):

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 = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.101-1613T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000435074.6	n.177-1613T>C		intron_variant, non_coding_transcript_variant
HLA-DPB2	ENST00000470997.1	n.101-1613T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40065 AN: 151824 Hom.: 5693 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.264 AC: 40063 AN: 151942 Hom.: 5690 Cov.: 31 AF XY: 0.261 AC XY: 19422 AN XY: 74272

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.307

Alfa AF: 0.300 Hom.: 12905

Bravo AF: 0.267

Asia WGS AF: 0.337 AC: 1174 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	4.3
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1810472; hg19: chr6-33083121;