rs3128917

Positions:

• chr6-33092219-T-G

Variant summary

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

The ENST00000433582.1(HLA-DPA2):​n.482A>C 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 0.352 in 194,578 control chromosomes in the GnomAD database, including 13,598 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 0.33 (9353 hom., cov: 32)
  • Exomes 𝑓: 0.43 (4245 hom.)
• Consequence: HLA-DPA2 ENST00000433582.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92

Genes affected

HLA-DPA2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-DPA2		n.33092219T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DPA2	ENST00000433582.1	n.482A>C		non_coding_transcript_exon_variant	3/4	6

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50026 AN: 151800 Hom.: 9327 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.317

GnomAD4 exome AF: 0.432 AC: 18417 AN: 42658 Hom.: 4245 Cov.: 0 AF XY: 0.434 AC XY: 10556 AN XY: 24310

Gnomad4 AFR exome AF: 0.606

Gnomad4 AMR exome AF: 0.320

Gnomad4 ASJ exome AF: 0.321

Gnomad4 EAS exome AF: 0.561

Gnomad4 SAS exome AF: 0.457

Gnomad4 FIN exome AF: 0.363

Gnomad4 NFE exome AF: 0.424

Gnomad4 OTH exome AF: 0.432

GnomAD4 genome AF: 0.330 AC: 50083 AN: 151920 Hom.: 9353 Cov.: 32 AF XY: 0.325 AC XY: 24139 AN XY: 74250

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.327

Alfa AF: 0.266 Hom.: 9667

Bravo AF: 0.334

Asia WGS AF: 0.397 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3128917; hg19: chr6-33059996;