rs3117004

chr6-33128989-A-G

Variant summary

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

The NR_001435.2(HLA-DPB2):n.757-76A>G 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 0.286 in 385,828 control chromosomes in the GnomAD database, including 17,209 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 (5920 hom., cov: 32)
  • Exomes 𝑓: 0.30 (11289 hom.)
• Consequence: HLA-DPB2 NR_001435.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLA-DPB2	NR_001435.2	n.757-76A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DPB2	ENST00000470997.1	n.757-76A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39910 AN: 152064 Hom.: 5924 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.262

GnomAD4 exome AF: 0.301 AC: 70361 AN: 233646 Hom.: 11289 AF XY: 0.301 AC XY: 40907 AN XY: 135844

Gnomad4 AFR exome AF: 0.132

Gnomad4 AMR exome AF: 0.189

Gnomad4 ASJ exome AF: 0.433

Gnomad4 EAS exome AF: 0.384

Gnomad4 SAS exome AF: 0.294

Gnomad4 FIN exome AF: 0.334

Gnomad4 NFE exome AF: 0.315

Gnomad4 OTH exome AF: 0.313

GnomAD4 genome AF: 0.262 AC: 39912 AN: 152182 Hom.: 5920 Cov.: 32 AF XY: 0.263 AC XY: 19548 AN XY: 74384

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.261

Alfa AF: 0.317 Hom.: 12882

Bravo AF: 0.249

Asia WGS AF: 0.341 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	4.2
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117004; hg19: chr6-33096766;