6-33096828-G-T

Variant names:

• chr6-33096828-G-T
• rs3117213
• ENST00000433582.1:n.55+413C>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.55+413C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,142 control chromosomes in the GnomAD database, including 9,414 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 (9414 hom., cov: 29)
• Consequence: HLA-DPA2 ENST00000433582.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 30 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 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.55+413C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.331 AC: 49988 AN: 151024 Hom.: 9391 Cov.: 29

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.331 AC: 50040 AN: 151142 Hom.: 9414 Cov.: 29 AF XY: 0.326 AC XY: 24095 AN XY: 73898

African (AFR) AF: 0.492 AC: 20207 AN: 41050

American (AMR) AF: 0.259 AC: 3944 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3466

East Asian (EAS) AF: 0.560 AC: 2868 AN: 5126

South Asian (SAS) AF: 0.251 AC: 1203 AN: 4798

European-Finnish (FIN) AF: 0.245 AC: 2563 AN: 10480

Middle Eastern (MID) AF: 0.210 AC: 61 AN: 290

European-Non Finnish (NFE) AF: 0.264 AC: 17840 AN: 67690

Other (OTH) AF: 0.332 AC: 696 AN: 2094

Alfa AF: 0.292 Hom.: 16864

Bravo AF: 0.339

Asia WGS AF: 0.389 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.70
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs3117213; hg19: chr6-33064605;