rs7764491

Positions:

• chr6-33093063-C-G

Variant summary

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

The ENST00000433582.1(HLA-DPA2):​n.130G>C 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 0.0538 in 152,490 control chromosomes in the GnomAD database, including 330 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 0.054 (330 hom., cov: 32)
  • Exomes 𝑓: 0.019 (0 hom.)
• Consequence: HLA-DPA2 ENST00000433582.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422

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=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0919 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.130G>C		non_coding_transcript_exon_variant	2/4

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8198 AN: 152216 Hom.: 330 Cov.: 32

Gnomad AFR AF: 0.0946

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0735

Gnomad SAS AF: 0.0801

Gnomad FIN AF: 0.00320

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0368

Gnomad OTH AF: 0.0702

GnomAD4 exome AF: 0.0192 AC: 3 AN: 156 Hom.: 0 Cov.: 0 AF XY: 0.0222 AC XY: 2 AN XY: 90

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0221

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0538 AC: 8197 AN: 152334 Hom.: 330 Cov.: 32 AF XY: 0.0518 AC XY: 3861 AN XY: 74496

Gnomad4 AFR AF: 0.0944

Gnomad4 AMR AF: 0.0457

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.0735

Gnomad4 SAS AF: 0.0800

Gnomad4 FIN AF: 0.00320

Gnomad4 NFE AF: 0.0368

Gnomad4 OTH AF: 0.0690

Alfa AF: 0.0421 Hom.: 23

Bravo AF: 0.0588

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	5.6
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7764491; hg19: chr6-33060840;