ENST00000469127.6:n.586-18455G>A

Variant names:

• chr13-50571020-G-A
• rs770389
• ENST00000469127.6:n.586-18455G>A

Variant summary

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

The ENST00000469127.6(DLEU1):​n.586-18455G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,046 control chromosomes in the GnomAD database, including 2,825 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 0.19 (2825 hom., cov: 31)
• Consequence: DLEU1 ENST00000469127.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 4 publications found

Genes affected

DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)

DLEU7 (HGNC:17567): (deleted in lymphocytic leukemia 7)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000469127.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000469127.6	TSL:5	n.586-18455G>A		intron	N/A
	DLEU1	ENST00000470726.7	TSL:5	n.346+137470G>A		intron	N/A
	DLEU1	ENST00000479420.5	TSL:5	n.458-18455G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28778 AN: 151926 Hom.: 2823 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.189 AC: 28786 AN: 152046 Hom.: 2825 Cov.: 31 AF XY: 0.189 AC XY: 14017 AN XY: 74298

African (AFR) AF: 0.187 AC: 7758 AN: 41476

American (AMR) AF: 0.169 AC: 2576 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 650 AN: 3466

East Asian (EAS) AF: 0.111 AC: 575 AN: 5182

South Asian (SAS) AF: 0.293 AC: 1411 AN: 4812

European-Finnish (FIN) AF: 0.133 AC: 1408 AN: 10578

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13712 AN: 67936

Other (OTH) AF: 0.210 AC: 443 AN: 2108

Alfa AF: 0.196 Hom.: 9055

Bravo AF: 0.188

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.43
DANN	Benign	0.63
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs770389; hg19: chr13-51145156;