rs3128918

Variant names:

• chr6-33093321-T-C
• rs3128918
• ENST00000433582.1:n.56-184A>G

Variant summary

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

The ENST00000433582.1(HLA-DPA2):​n.56-184A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,174 control chromosomes in the GnomAD database, including 2,840 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 (2840 hom., cov: 32)
• Consequence: HLA-DPA2 ENST00000433582.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 33 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DPA2	ENST00000433582.1	TSL:6	n.56-184A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27372 AN: 152056 Hom.: 2836 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0577

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.190

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.180 AC: 27395 AN: 152174 Hom.: 2840 Cov.: 32 AF XY: 0.184 AC XY: 13707 AN XY: 74364

African (AFR) AF: 0.135 AC: 5586 AN: 41524

American (AMR) AF: 0.309 AC: 4725 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3470

East Asian (EAS) AF: 0.0584 AC: 303 AN: 5184

South Asian (SAS) AF: 0.139 AC: 673 AN: 4826

European-Finnish (FIN) AF: 0.249 AC: 2629 AN: 10566

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12091 AN: 68000

Other (OTH) AF: 0.187 AC: 394 AN: 2112

Alfa AF: 0.181 Hom.: 8165

Bravo AF: 0.188

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	-0.96
CADD	Benign	2.0
DANN	Benign	0.60
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs3128918; hg19: chr6-33061098;