rs2281388

Variant names:

• chr6-33092341-G-A
• rs2281388
• ENST00000433582.1:n.360C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-33092341-G-A
• chr6-33092341-G-C
• chr6-33092341-G-T

Variant summary

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

The ENST00000433582.1(HLA-DPA2):​n.360C>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 0.0354 in 242,390 control chromosomes in the GnomAD database, including 1,074 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 0.031 (509 hom., cov: 32)
  • Exomes 𝑓: 0.043 (565 hom.)
• Consequence: HLA-DPA2 ENST00000433582.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.14

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=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPA2		n.33092341G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DPA2	ENST00000433582.1	n.360C>T		non_coding_transcript_exon_variant	Exon 3 of 4	6

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 4674 AN: 152180 Hom.: 498 Cov.: 32

Gnomad AFR AF: 0.00664

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0220

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0217

Gnomad OTH AF: 0.0335

GnomAD4 exome AF: 0.0431 AC: 3882 AN: 90092 Hom.: 565 Cov.: 0 AF XY: 0.0413 AC XY: 2123 AN XY: 51356

Gnomad4 AFR exome AF: 0.00487

Gnomad4 AMR exome AF: 0.0222

Gnomad4 ASJ exome AF: 0.0104

Gnomad4 EAS exome AF: 0.347

Gnomad4 SAS exome AF: 0.0177

Gnomad4 FIN exome AF: 0.0232

Gnomad4 NFE exome AF: 0.0240

Gnomad4 OTH exome AF: 0.0417

GnomAD4 genome AF: 0.0308 AC: 4695 AN: 152298 Hom.: 509 Cov.: 32 AF XY: 0.0323 AC XY: 2402 AN XY: 74472

Gnomad4 AFR AF: 0.00662

Gnomad4 AMR AF: 0.0221

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.0240

Gnomad4 NFE AF: 0.0217

Gnomad4 OTH AF: 0.0436

Alfa AF: 0.0244 Hom.: 332

Bravo AF: 0.0312

Asia WGS AF: 0.131 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	12
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: rs2281388; hg19: chr6-33060118;