rs3129272

chr6-33128649-C-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.661C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 193,204 control chromosomes in the GnomAD database, including 7,798 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 (5914 hom., cov: 32)
  • Exomes 𝑓: 0.29 (1884 hom.)
• Consequence: HLA-DPB2 NR_001435.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631

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=-0.86).
• 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.661C>T		non_coding_transcript_exon_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-DPB2	ENST00000470997.1	n.661C>T		non_coding_transcript_exon_variant	4/5

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39864 AN: 151950 Hom.: 5918 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: 0.383

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.262

GnomAD4 exome AF: 0.294 AC: 12075 AN: 41136 Hom.: 1884 Cov.: 0 AF XY: 0.298 AC XY: 6773 AN XY: 22742

Gnomad4 AFR exome AF: 0.107

Gnomad4 AMR exome AF: 0.166

Gnomad4 ASJ exome AF: 0.402

Gnomad4 EAS exome AF: 0.394

Gnomad4 SAS exome AF: 0.273

Gnomad4 FIN exome AF: 0.350

Gnomad4 NFE exome AF: 0.287

Gnomad4 OTH exome AF: 0.306

GnomAD4 genome AF: 0.262 AC: 39866 AN: 152068 Hom.: 5914 Cov.: 32 AF XY: 0.262 AC XY: 19511 AN XY: 74332

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: 0.330

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.260

Alfa AF: 0.297 Hom.: 1411

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	-0.86
Cadd	Benign	9.3
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129272; hg19: chr6-33096426; COSMIC: COSV71039912;