ENST00000433582.1:n.360C>T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 59 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433582.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DPA2	ENST00000433582.1	TSL:6	n.360C>T		non_coding_transcript_exon	Exon 3 of 4

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

African (AFR) AF: 0.00487 AC: 15 AN: 3080

American (AMR) AF: 0.0222 AC: 98 AN: 4418

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 14 AN: 1342

East Asian (EAS) AF: 0.347 AC: 1931 AN: 5560

South Asian (SAS) AF: 0.0177 AC: 130 AN: 7348

European-Finnish (FIN) AF: 0.0232 AC: 288 AN: 12440

Middle Eastern (MID) AF: 0.00940 AC: 11 AN: 1170

European-Non Finnish (NFE) AF: 0.0240 AC: 1200 AN: 50060

Other (OTH) AF: 0.0417 AC: 195 AN: 4674

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

African (AFR) AF: 0.00662 AC: 275 AN: 41562

American (AMR) AF: 0.0221 AC: 338 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2109 AN: 5176

South Asian (SAS) AF: 0.0228 AC: 110 AN: 4828

European-Finnish (FIN) AF: 0.0240 AC: 255 AN: 10624

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0217 AC: 1475 AN: 68010

Other (OTH) AF: 0.0436 AC: 92 AN: 2112

Alfa AF: 0.0267 Hom.: 1114

Bravo AF: 0.0312

Asia WGS AF: 0.131 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs2281388; hg19: chr6-33060118;