rs2281389

Positions:

• chr6-33092019-A-G

Variant summary

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

The ENST00000433582.1(HLA-DPA2):​n.582+100T>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 0.141 in 156,028 control chromosomes in the GnomAD database, including 1,717 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 0.14 (1589 hom., cov: 32)
  • Exomes 𝑓: 0.24 (128 hom.)
• Consequence: HLA-DPA2 ENST00000433582.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

Genes affected

HLA-DPA2 (HGNC:4939): (major histocompatibility complex, class II, DP alpha 2 (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DPA2	ENST00000433582.1	n.582+100T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21148 AN: 152080 Hom.: 1590 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.144

GnomAD4 exome AF: 0.242 AC: 928 AN: 3830 Hom.: 128 Cov.: 0 AF XY: 0.226 AC XY: 506 AN XY: 2236

Gnomad4 AFR exome AF: 0.0641

Gnomad4 AMR exome AF: 0.224

Gnomad4 ASJ exome AF: 0.188

Gnomad4 EAS exome AF: 0.325

Gnomad4 SAS exome AF: 0.304

Gnomad4 FIN exome AF: 0.197

Gnomad4 NFE exome AF: 0.259

Gnomad4 OTH exome AF: 0.209

GnomAD4 genome AF: 0.139 AC: 21148 AN: 152198 Hom.: 1589 Cov.: 32 AF XY: 0.138 AC XY: 10293 AN XY: 74408

Gnomad4 AFR AF: 0.0737

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.145

Alfa AF: 0.164 Hom.: 3690

Bravo AF: 0.132

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2281389; hg19: chr6-33059796;