6-33128989-A-G

Variant names:

• chr6-33128989-A-G
• rs3117004
• ENST00000782902.1:n.1381A>G

Variant summary

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

The ENST00000782902.1(ENSG00000291111):​n.1381A>G 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 0.286 in 385,828 control chromosomes in the GnomAD database, including 17,209 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 0.26 (5920 hom., cov: 32)
  • Exomes 𝑓: 0.30 (11289 hom.)
• Consequence: ENSG00000291111 ENST00000782902.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 32 publications found

Genes affected

ENSG00000291111 (HGNC:):

HLA-DPB2 (HGNC:4941): (major histocompatibility complex, class II, DP beta 2 (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.757-76A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291111	ENST00000782902.1	n.1381A>G		non_coding_transcript_exon_variant	Exon 2 of 2
HLA-DPB2	ENST00000470997.1	n.757-76A>G		intron_variant	Intron 4 of 4	6
ENSG00000291111	ENST00000782892.1	n.429+11769A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39910 AN: 152064 Hom.: 5924 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.262

GnomAD4 exome AF: 0.301 AC: 70361 AN: 233646 Hom.: 11289 AF XY: 0.301 AC XY: 40907 AN XY: 135844

African (AFR) AF: 0.132 AC: 749 AN: 5676

American (AMR) AF: 0.189 AC: 4400 AN: 23292

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 2816 AN: 6506

East Asian (EAS) AF: 0.384 AC: 2690 AN: 7014

South Asian (SAS) AF: 0.294 AC: 12060 AN: 41012

European-Finnish (FIN) AF: 0.334 AC: 6148 AN: 18420

Middle Eastern (MID) AF: 0.321 AC: 769 AN: 2396

European-Non Finnish (NFE) AF: 0.315 AC: 37379 AN: 118618

Other (OTH) AF: 0.313 AC: 3350 AN: 10712

GnomAD4 genome AF: 0.262 AC: 39912 AN: 152182 Hom.: 5920 Cov.: 32 AF XY: 0.263 AC XY: 19548 AN XY: 74384

African (AFR) AF: 0.131 AC: 5436 AN: 41530

American (AMR) AF: 0.245 AC: 3748 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1521 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1979 AN: 5176

South Asian (SAS) AF: 0.309 AC: 1493 AN: 4830

European-Finnish (FIN) AF: 0.331 AC: 3503 AN: 10582

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.315 AC: 21437 AN: 67986

Other (OTH) AF: 0.261 AC: 550 AN: 2110

Alfa AF: 0.303 Hom.: 27485

Bravo AF: 0.249

Asia WGS AF: 0.341 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.31
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3117004; hg19: chr6-33096766; COSMIC: COSV107528482;