13-50267187-C-T

Variant names:

• chr13-50267187-C-T
• rs806321
• ENST00000461527.7:n.441-7745C>T

Variant summary

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

The ENST00000461527.7(DLEU1):​n.441-7745C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,846 control chromosomes in the GnomAD database, including 17,659 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 0.47 (17659 hom., cov: 31)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 28 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	NR_109974.1		n.443-123011C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000461527.7	TSL:1	n.441-7745C>T		intron	N/A
	DLEU1	ENST00000463474.7	TSL:1	n.441-71489C>T		intron	N/A
	DLEU1	ENST00000468168.6	TSL:1	n.441-123011C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71501 AN: 151728 Hom.: 17669 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.471 AC: 71488 AN: 151846 Hom.: 17659 Cov.: 31 AF XY: 0.470 AC XY: 34900 AN XY: 74182

African (AFR) AF: 0.349 AC: 14442 AN: 41416

American (AMR) AF: 0.394 AC: 6009 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1855 AN: 3464

East Asian (EAS) AF: 0.733 AC: 3778 AN: 5156

South Asian (SAS) AF: 0.411 AC: 1975 AN: 4800

European-Finnish (FIN) AF: 0.593 AC: 6253 AN: 10536

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.525 AC: 35666 AN: 67904

Other (OTH) AF: 0.488 AC: 1028 AN: 2108

Alfa AF: 0.513 Hom.: 87108

Bravo AF: 0.457

Asia WGS AF: 0.490 AC: 1703 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	2.4
DANN	Benign	0.71
PhyloP100		0.016

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs806321;

hg19: chr13-50841323;