ENST00000461527.7:n.440+80539T>C

Variant names:

• chr13-50163733-T-C
• rs1798968
• ENST00000461527.7:n.440+80539T>C

Variant summary

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

The ENST00000461527.7(DLEU1):​n.440+80539T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,946 control chromosomes in the GnomAD database, including 25,070 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 0.56 (25070 hom., cov: 31)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000461527.7. 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
	DLEU1	NR_109974.1		n.442+80539T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000461527.7	TSL:1	n.440+80539T>C		intron	N/A
	DLEU1	ENST00000463474.7	TSL:1	n.440+80539T>C		intron	N/A
	DLEU1	ENST00000468168.6	TSL:1	n.440+80539T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85667 AN: 151828 Hom.: 25070 Cov.: 31

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.564 AC: 85690 AN: 151946 Hom.: 25070 Cov.: 31 AF XY: 0.567 AC XY: 42074 AN XY: 74256

African (AFR) AF: 0.418 AC: 17299 AN: 41420

American (AMR) AF: 0.515 AC: 7870 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2450 AN: 3466

East Asian (EAS) AF: 0.771 AC: 3985 AN: 5168

South Asian (SAS) AF: 0.776 AC: 3744 AN: 4822

European-Finnish (FIN) AF: 0.598 AC: 6306 AN: 10542

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41936 AN: 67944

Other (OTH) AF: 0.578 AC: 1219 AN: 2110

Alfa AF: 0.593 Hom.: 88650

Bravo AF: 0.547

Asia WGS AF: 0.723 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.74
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1798968; hg19: chr13-50737869;