rs733208

Positions:

• chr6-33114531-G-A
• chr6-33114531-G-T

Variant summary

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

The NR_001435.2(HLA-DPB2):​n.100+1916G>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 0.132 in 152,184 control chromosomes in the GnomAD database, including 1,599 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 0.13 (1599 hom., cov: 32)
• Consequence: HLA-DPB2 NR_001435.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.100+1916G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000435074.6	n.176+1916G>A		intron_variant, non_coding_transcript_variant
HLA-DPB2	ENST00000470997.1	n.100+1916G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20089 AN: 152066 Hom.: 1602 Cov.: 32

Gnomad AFR AF: 0.0560

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.132 AC: 20082 AN: 152184 Hom.: 1599 Cov.: 32 AF XY: 0.133 AC XY: 9875 AN XY: 74386

Gnomad4 AFR AF: 0.0560

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.142

Alfa AF: 0.144 Hom.: 585

Bravo AF: 0.127

Asia WGS AF: 0.192 AC: 670 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	4.6
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs733208; hg19: chr6-33082308;