6-33092019-A-G

Variant names:

• chr6-33092019-A-G
• rs2281389

Variant summary

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

The variant allele was found at a frequency of 0.141 in 156,028 control chromosomes in the GnomAD database, including 1,717 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 0.14 (1589 hom., cov: 32)
  • Exomes 𝑓: 0.24 (128 hom.)
• Consequence: HLA-DPA2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 54 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPA2		n.33092019A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DPA2	ENST00000433582.1	n.582+100T>C		intron_variant	Intron 3 of 3	6

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21148 AN: 152080 Hom.: 1590 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.144

GnomAD4 exome AF: 0.242 AC: 928 AN: 3830 Hom.: 128 Cov.: 0 AF XY: 0.226 AC XY: 506 AN XY: 2236

African (AFR) AF: 0.0641 AC: 5 AN: 78

American (AMR) AF: 0.224 AC: 22 AN: 98

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 15 AN: 80

East Asian (EAS) AF: 0.325 AC: 76 AN: 234

South Asian (SAS) AF: 0.304 AC: 48 AN: 158

European-Finnish (FIN) AF: 0.197 AC: 139 AN: 706

Middle Eastern (MID) AF: 0.179 AC: 5 AN: 28

European-Non Finnish (NFE) AF: 0.259 AC: 552 AN: 2132

Other (OTH) AF: 0.209 AC: 66 AN: 316

GnomAD4 genome AF: 0.139 AC: 21148 AN: 152198 Hom.: 1589 Cov.: 32 AF XY: 0.138 AC XY: 10293 AN XY: 74408

African (AFR) AF: 0.0737 AC: 3059 AN: 41530

American (AMR) AF: 0.150 AC: 2293 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3468

East Asian (EAS) AF: 0.133 AC: 689 AN: 5172

South Asian (SAS) AF: 0.164 AC: 789 AN: 4824

European-Finnish (FIN) AF: 0.168 AC: 1781 AN: 10600

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11738 AN: 67992

Other (OTH) AF: 0.145 AC: 306 AN: 2110

Alfa AF: 0.159 Hom.: 8137

Bravo AF: 0.132

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.78
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2281389; hg19: chr6-33059796;