chr13-50532419-C-T

Variant names:

• chr13-50532419-C-T
• rs1239947
• ENST00000460525.6:n.363-774C>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000460525.6	n.363-774C>T		intron_variant	Intron 3 of 3	1
DLEU1	ENST00000462427.2	n.452-774C>T		intron_variant	Intron 3 of 3	1
DLEU1	ENST00000470726.7	n.346+98869C>T		intron_variant	Intron 3 of 5	5

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;