rs1883414

Positions:

• chr6-33118671-G-A
• chr6-33118671-G-T

Variant summary

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

The ENST00000435074.6(ENSG00000291111):​n.721G>A 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 0.283 in 152,360 control chromosomes in the GnomAD database, including 6,220 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 0.28 (6211 hom., cov: 32)
  • Exomes 𝑓: 0.27 (9 hom.)
• Consequence: ENST00000435074.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.364+1451G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000435074.6	n.721G>A		non_coding_transcript_exon_variant	3/3
HLA-DPB2	ENST00000470997.1	n.364+1451G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43011 AN: 151984 Hom.: 6212 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.292

GnomAD4 exome AF: 0.271 AC: 70 AN: 258 Hom.: 9 Cov.: 0 AF XY: 0.294 AC XY: 53 AN XY: 180

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.254

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.283 AC: 43028 AN: 152102 Hom.: 6211 Cov.: 32 AF XY: 0.283 AC XY: 21067 AN XY: 74370

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.291

Alfa AF: 0.306 Hom.: 7219

Bravo AF: 0.277

Asia WGS AF: 0.316 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1883414; hg19: chr6-33086448;