ENST00000435074.7:n.208-1546A>G

Variant names:

• chr6-33115411-A-G
• rs6457715
• ENST00000435074.7:n.208-1546A>G

Variant summary

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

The ENST00000435074.7(ENSG00000291111):​n.208-1546A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 151,998 control chromosomes in the GnomAD database, including 11,044 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 0.35 (11044 hom., cov: 31)
• Consequence: ENSG00000291111 ENST00000435074.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.101-1546A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291111	ENST00000435074.7	n.208-1546A>G		intron_variant	Intron 1 of 2	6
HLA-DPB2	ENST00000470997.1	n.101-1546A>G		intron_variant	Intron 1 of 4	6
ENSG00000291111	ENST00000782892.1	n.166-1546A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52379 AN: 151880 Hom.: 11005 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.345 AC: 52472 AN: 151998 Hom.: 11044 Cov.: 31 AF XY: 0.346 AC XY: 25712 AN XY: 74306

African (AFR) AF: 0.574 AC: 23760 AN: 41400

American (AMR) AF: 0.378 AC: 5774 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3470

East Asian (EAS) AF: 0.535 AC: 2769 AN: 5172

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4820

European-Finnish (FIN) AF: 0.275 AC: 2900 AN: 10564

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14810 AN: 67978

Other (OTH) AF: 0.333 AC: 700 AN: 2102

Alfa AF: 0.257 Hom.: 4258

Bravo AF: 0.369

Asia WGS AF: 0.363 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6457715; hg19: chr6-33083188;