ENST00000433582.1:n.482A>C

Variant names:

• chr6-33092219-T-G
• rs3128917
• ENST00000433582.1:n.482A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 55 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=-0.66).
• 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 rank	MANE	Protein	UniProt
HLA-DPA2		n.33092219T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DPA2	ENST00000433582.1	n.482A>C		non_coding_transcript_exon_variant	Exon 3 of 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

African (AFR) AF: 0.606 AC: 905 AN: 1494

American (AMR) AF: 0.320 AC: 572 AN: 1786

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 243 AN: 758

East Asian (EAS) AF: 0.561 AC: 1822 AN: 3248

South Asian (SAS) AF: 0.457 AC: 1914 AN: 4188

European-Finnish (FIN) AF: 0.363 AC: 1251 AN: 3442

Middle Eastern (MID) AF: 0.324 AC: 271 AN: 836

European-Non Finnish (NFE) AF: 0.424 AC: 10368 AN: 24426

Other (OTH) AF: 0.432 AC: 1071 AN: 2480

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

African (AFR) AF: 0.485 AC: 20088 AN: 41406

American (AMR) AF: 0.256 AC: 3910 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3468

East Asian (EAS) AF: 0.565 AC: 2913 AN: 5160

South Asian (SAS) AF: 0.262 AC: 1259 AN: 4812

European-Finnish (FIN) AF: 0.249 AC: 2628 AN: 10568

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.263 AC: 17873 AN: 67908

Other (OTH) AF: 0.327 AC: 689 AN: 2110

Alfa AF: 0.282 Hom.: 25867

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
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs3128917; hg19: chr6-33059996;