6-33094896-G-T

Variant names:

• chr6-33094896-G-T
• rs2395314
• ENST00000433582.1:n.56-1759C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433582.1(HLA-DPA2):​n.56-1759C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,060 control chromosomes in the GnomAD database, including 9,358 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 (9358 hom., cov: 32)
• Consequence: HLA-DPA2 ENST00000433582.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

Genes affected

HLA-DPA2 (HGNC:4939): (major histocompatibility complex, class II, DP alpha 2 (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DPA2	ENST00000433582.1	n.56-1759C>A		intron_variant	Intron 1 of 3	6

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50070 AN: 151942 Hom.: 9335 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.330 AC: 50123 AN: 152060 Hom.: 9358 Cov.: 32 AF XY: 0.325 AC XY: 24152 AN XY: 74326

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.327

Alfa AF: 0.256 Hom.: 4517

Bravo AF: 0.334

Asia WGS AF: 0.396 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395314; hg19: chr6-33062673;