rs1798968

chr13-50163733-T-C

Variant summary

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

The NR_109974.1(DLEU1):n.442+80539T>C 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 0.564 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 NR_109974.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLEU1	NR_109974.1	n.442+80539T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU1	ENST00000490577.5	n.1637+5657T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.578

Alfa AF: 0.602 Hom.: 41138

Bravo AF: 0.547

Asia WGS AF: 0.723 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.8
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1798968; hg19: chr13-50737869;