ENST00000435074.7:n.207+1916G>A

Variant names:

• chr6-33114531-G-A
• rs733208
• ENST00000435074.7:n.207+1916G>A

Variant summary

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

The ENST00000435074.7(ENSG00000291111):​n.207+1916G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,184 control chromosomes in the GnomAD database, including 1,599 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 0.13 (1599 hom., cov: 32)
• Consequence: ENSG00000291111 ENST00000435074.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 25 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-DPB2	NR_001435.2	n.100+1916G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291111	ENST00000435074.7	n.207+1916G>A		intron_variant	Intron 1 of 2	6
HLA-DPB2	ENST00000470997.1	n.100+1916G>A		intron_variant	Intron 1 of 4	6
ENSG00000291111	ENST00000782892.1	n.165+1916G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20089 AN: 152066 Hom.: 1602 Cov.: 32

Gnomad AFR AF: 0.0560

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.132 AC: 20082 AN: 152184 Hom.: 1599 Cov.: 32 AF XY: 0.133 AC XY: 9875 AN XY: 74386

African (AFR) AF: 0.0560 AC: 2323 AN: 41518

American (AMR) AF: 0.124 AC: 1901 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 925 AN: 3470

East Asian (EAS) AF: 0.233 AC: 1203 AN: 5174

South Asian (SAS) AF: 0.161 AC: 777 AN: 4826

European-Finnish (FIN) AF: 0.158 AC: 1671 AN: 10582

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10813 AN: 68006

Other (OTH) AF: 0.142 AC: 300 AN: 2114

Alfa AF: 0.147 Hom.: 3607

Bravo AF: 0.127

Asia WGS AF: 0.192 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.27
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs733208; hg19: chr6-33082308;