rs3117027

Variant names:

• chr6-33121846-C-A
• rs3117027
• ENST00000470997.1:n.364+4626C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-33121846-C-A
• chr6-33121846-C-G
• chr6-33121846-C-T

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.364+4626C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,088 control chromosomes in the GnomAD database, including 7,063 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 0.30 (7063 hom., cov: 32)
• Consequence: HLA-DPB2 NR_001435.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.915
• Publications: 32 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.509 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.364+4626C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DPB2	ENST00000470997.1	TSL:6	n.364+4626C>A		intron	N/A
	ENSG00000291111	ENST00000782892.1		n.429+4626C>A		intron	N/A
	ENSG00000291111	ENST00000782893.1		n.403+4626C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45552 AN: 151970 Hom.: 7063 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.300 AC: 45568 AN: 152088 Hom.: 7063 Cov.: 32 AF XY: 0.300 AC XY: 22337 AN XY: 74364

African (AFR) AF: 0.241 AC: 10007 AN: 41476

American (AMR) AF: 0.249 AC: 3809 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1411 AN: 3466

East Asian (EAS) AF: 0.199 AC: 1030 AN: 5176

South Asian (SAS) AF: 0.527 AC: 2536 AN: 4816

European-Finnish (FIN) AF: 0.281 AC: 2978 AN: 10580

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22706 AN: 67974

Other (OTH) AF: 0.306 AC: 644 AN: 2106

Alfa AF: 0.317 Hom.: 7203

Bravo AF: 0.288

Asia WGS AF: 0.346 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs3117027; hg19: chr6-33089623;