rs3128917

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.

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.482A>C		non_coding_transcript_exon	Exon 3 of 4

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 v4.9

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

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

Other links and lift over

dbSNP: rs3128917;

hg19: chr6-33059996;