6-33115344-T-C

Variant names:

• chr6-33115344-T-C
• rs1810472
• ENST00000435074.7:n.208-1613T>C

Variant summary

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

The NR_001435.2(HLA-DPB2):​n.101-1613T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,942 control chromosomes in the GnomAD database, including 5,690 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 (5690 hom., cov: 31)
• Consequence: HLA-DPB2 NR_001435.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 36 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_001435.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DPB2	NR_001435.2		n.101-1613T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291111	ENST00000435074.7	TSL:6	n.208-1613T>C		intron	N/A
	HLA-DPB2	ENST00000470997.1	TSL:6	n.101-1613T>C		intron	N/A
	ENSG00000291111	ENST00000782892.1		n.166-1613T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40065 AN: 151824 Hom.: 5693 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.264 AC: 40063 AN: 151942 Hom.: 5690 Cov.: 31 AF XY: 0.261 AC XY: 19422 AN XY: 74272

African (AFR) AF: 0.191 AC: 7923 AN: 41434

American (AMR) AF: 0.287 AC: 4383 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1799 AN: 3470

East Asian (EAS) AF: 0.314 AC: 1624 AN: 5166

South Asian (SAS) AF: 0.359 AC: 1729 AN: 4818

European-Finnish (FIN) AF: 0.212 AC: 2235 AN: 10560

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19432 AN: 67922

Other (OTH) AF: 0.307 AC: 645 AN: 2104

Alfa AF: 0.287 Hom.: 28002

Bravo AF: 0.267

Asia WGS AF: 0.337 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.39
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs1810472; hg19: chr6-33083121;