13-50532419-C-T

Variant names:

• chr13-50532419-C-T
• rs1239947
• ENST00000460525.6:n.363-774C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000469127.6	n.585+26739C>T		intron_variant	Intron 5 of 6	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

African (AFR) AF: 0.628 AC: 26042 AN: 41460

American (AMR) AF: 0.739 AC: 11283 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2447 AN: 3470

East Asian (EAS) AF: 0.855 AC: 4425 AN: 5178

South Asian (SAS) AF: 0.548 AC: 2641 AN: 4818

European-Finnish (FIN) AF: 0.743 AC: 7870 AN: 10590

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44779 AN: 67816

Other (OTH) AF: 0.657 AC: 1389 AN: 2114

Alfa AF: 0.667 Hom.: 147959

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1239947; hg19: chr13-51106555;