6-33091892-G-T

Variant names:

• chr6-33091892-G-T
• rs2281390
• ENST00000433582.1:n.594C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433582.1(HLA-DPA2):​n.594C>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 0.179 in 152,840 control chromosomes in the GnomAD database, including 2,825 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 0.18 (2808 hom., cov: 32)
  • Exomes 𝑓: 0.21 (17 hom.)
• Consequence: HLA-DPA2 ENST00000433582.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667
• Publications: 35 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.301 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.594C>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27191 AN: 152080 Hom.: 2804 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0578

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.187

GnomAD4 exome AF: 0.207 AC: 133 AN: 642 Hom.: 17 Cov.: 0 AF XY: 0.198 AC XY: 84 AN XY: 424

African (AFR) AF: 0.125 AC: 1 AN: 8

American (AMR) AF: 0.833 AC: 5 AN: 6

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.229 AC: 78 AN: 340

Middle Eastern (MID) AF: 0.333 AC: 2 AN: 6

European-Non Finnish (NFE) AF: 0.174 AC: 45 AN: 258

Other (OTH) AF: 0.0909 AC: 2 AN: 22

GnomAD4 genome AF: 0.179 AC: 27214 AN: 152198 Hom.: 2808 Cov.: 32 AF XY: 0.183 AC XY: 13619 AN XY: 74396

African (AFR) AF: 0.131 AC: 5461 AN: 41536

American (AMR) AF: 0.308 AC: 4710 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3466

East Asian (EAS) AF: 0.0586 AC: 303 AN: 5174

South Asian (SAS) AF: 0.140 AC: 674 AN: 4828

European-Finnish (FIN) AF: 0.248 AC: 2623 AN: 10582

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12065 AN: 67998

Other (OTH) AF: 0.183 AC: 388 AN: 2116

Alfa AF: 0.179 Hom.: 11328

Bravo AF: 0.186

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.0
DANN	Benign	0.67
PhyloP100		0.67

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2281390;

hg19: chr6-33059669;