rs3129272

Variant names:

• chr6-33128649-C-T
• rs3129272
• ENST00000470997.1:n.661C>T

Variant summary

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

The ENST00000470997.1(HLA-DPB2):​n.661C>T 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 0.269 in 193,204 control chromosomes in the GnomAD database, including 7,798 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 (5914 hom., cov: 32)
  • Exomes 𝑓: 0.29 (1884 hom.)
• Consequence: HLA-DPB2 ENST00000470997.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 3 publications found

Genes affected

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

ENSG00000291111 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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.661C>T		non_coding_transcript_exon_variant	Exon 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-DPB2	ENST00000470997.1	n.661C>T		non_coding_transcript_exon_variant	Exon 4 of 5	6
ENSG00000291111	ENST00000782894.1	n.133C>T		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000291111	ENST00000782895.1	n.167C>T		non_coding_transcript_exon_variant	Exon 2 of 5

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39864 AN: 151950 Hom.: 5918 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: 0.383

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.262

GnomAD4 exome AF: 0.294 AC: 12075 AN: 41136 Hom.: 1884 Cov.: 0 AF XY: 0.298 AC XY: 6773 AN XY: 22742

African (AFR) AF: 0.107 AC: 80 AN: 750

American (AMR) AF: 0.166 AC: 522 AN: 3136

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 151 AN: 376

East Asian (EAS) AF: 0.394 AC: 626 AN: 1590

South Asian (SAS) AF: 0.273 AC: 925 AN: 3394

European-Finnish (FIN) AF: 0.350 AC: 3279 AN: 9368

Middle Eastern (MID) AF: 0.252 AC: 51 AN: 202

European-Non Finnish (NFE) AF: 0.287 AC: 5903 AN: 20564

Other (OTH) AF: 0.306 AC: 538 AN: 1756

GnomAD4 genome AF: 0.262 AC: 39866 AN: 152068 Hom.: 5914 Cov.: 32 AF XY: 0.262 AC XY: 19511 AN XY: 74332

African (AFR) AF: 0.131 AC: 5426 AN: 41496

American (AMR) AF: 0.245 AC: 3742 AN: 15276

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

East Asian (EAS) AF: 0.382 AC: 1968 AN: 5158

South Asian (SAS) AF: 0.309 AC: 1487 AN: 4814

European-Finnish (FIN) AF: 0.330 AC: 3491 AN: 10568

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21435 AN: 67966

Other (OTH) AF: 0.260 AC: 550 AN: 2114

Alfa AF: 0.248 Hom.: 1556

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	-0.86
CADD	Benign	9.3
DANN	Benign	0.36
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs3129272; hg19: chr6-33096426; COSMIC: COSV71039912;