ENST00000621282.4:n.1830-690G>A

Variant names:

• chr13-49989311-C-T
• rs9596219
• ENST00000621282.4:n.1830-690G>A

Variant summary

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

The ENST00000621282.4(DLEU2):​n.1830-690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,814 control chromosomes in the GnomAD database, including 3,555 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 0.20 (3555 hom., cov: 31)
• Consequence: DLEU2 ENST00000621282.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520
• Publications: 21 publications found

Genes affected

DLEU2 (HGNC:13748): (deleted in lymphocytic leukemia 2) This locus represents a microRNA host gene and also produces long alternatively spliced non-coding RNAs. This genome region was observed to be deleted or epigenetically suppressed in leukemia, and was implicated as a negative regulator of cell proliferation. However, an alternative transcript produced at this locus was also found to promote progression through the cell cycle via angiotensin I converting enzyme 2 and cyclin D1. [provided by RefSeq, Dec 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000621282.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU2	NR_152566.1		n.1830-690G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU2	ENST00000621282.4	TSL:1	n.1830-690G>A		intron	N/A
	DLEU2	ENST00000651713.2		n.1048+4482G>A		intron	N/A
	DLEU2	ENST00000658343.1		n.232+4482G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29872 AN: 151698 Hom.: 3557 Cov.: 31

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.197 AC: 29884 AN: 151814 Hom.: 3555 Cov.: 31 AF XY: 0.196 AC XY: 14557 AN XY: 74202

African (AFR) AF: 0.0761 AC: 3153 AN: 41418

American (AMR) AF: 0.195 AC: 2971 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3462

East Asian (EAS) AF: 0.337 AC: 1738 AN: 5152

South Asian (SAS) AF: 0.119 AC: 573 AN: 4822

European-Finnish (FIN) AF: 0.254 AC: 2666 AN: 10504

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17211 AN: 67906

Other (OTH) AF: 0.187 AC: 393 AN: 2102

Alfa AF: 0.228 Hom.: 12908

Bravo AF: 0.191

Asia WGS AF: 0.209 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.4
DANN	Benign	0.62
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs9596219; hg19: chr13-50563447;