6-33093093-G-T

Position:

• chr6-33093093-G-T

Variant summary

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

The ENST00000433582.1(HLA-DPA2):​n.100C>A 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 0.143 in 152,368 control chromosomes in the GnomAD database, including 1,684 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 (1684 hom., cov: 32)
  • Exomes 𝑓: 0.12 (0 hom.)
• Consequence: HLA-DPA2 ENST00000433582.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-DPA2	ENST00000433582.1	n.100C>A		non_coding_transcript_exon_variant	2/4

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21689 AN: 152158 Hom.: 1679 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.156

GnomAD4 exome AF: 0.120 AC: 11 AN: 92 Hom.: 0 Cov.: 0 AF XY: 0.173 AC XY: 9 AN XY: 52

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.128

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.143 AC: 21717 AN: 152276 Hom.: 1684 Cov.: 32 AF XY: 0.145 AC XY: 10788 AN XY: 74442

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.155

Alfa AF: 0.131 Hom.: 449

Bravo AF: 0.145

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2295119; hg19: chr6-33060870;