13-50532419-C-T

Variant summary

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

The ENST00000460525.6(DLEU1):n.363-774C>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 0.67 in 151,922 control chromosomes in the GnomAD database, including 34,294 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 0.67 (34294 hom., cov: 32)
• Consequence: DLEU1 ENST00000460525.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU1	ENST00000460525.6	n.363-774C>T		intron_variant, non_coding_transcript_variant		1
DLEU1	ENST00000462427.2	n.452-774C>T		intron_variant, non_coding_transcript_variant		1
DLEU7	ENST00000651397.1	c.*572-6412G>A		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101710 AN: 151804 Hom.: 34275 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.670 AC: 101777 AN: 151922 Hom.: 34294 Cov.: 32 AF XY: 0.670 AC XY: 49776 AN XY: 74272

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.657

Alfa AF: 0.669 Hom.: 74954

Bravo AF: 0.672

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.4
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1239947; hg19: chr13-51106555;