13-50492487-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109974.1(DLEU1):n.675-164C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 151,336 control chromosomes in the GnomAD database, including 41,556 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 0.74 (41556 hom., cov: 32)
• Consequence: DLEU1 NR_109974.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLEU1	NR_109974.1	n.675-164C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU1	ENST00000490577.5	n.1776-164C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.740 AC: 111954 AN: 151218 Hom.: 41504 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.741 AC: 112067 AN: 151336 Hom.: 41556 Cov.: 32 AF XY: 0.742 AC XY: 54873 AN XY: 73952

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.851

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.742

Alfa AF: 0.743 Hom.: 11454

Bravo AF: 0.743

Asia WGS AF: 0.838 AC: 2912 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.48
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1262778; hg19: chr13-51066623;