Genetic Variant DLEU1:n.252-164C>T (chr13-50492487-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000460525.6(DLEU1):n.252-164C>T variant causes a intron 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
ENST00000460525.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.228

Publications

14 publications found

Variant links:

Genes affected

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

DLEU1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DLEU1	NR_109974.1 link	n.675-164C>T		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000460525.6 link	n.252-164C>T	intron_variant	Intron 2 of 3	1
DLEU1	ENST00000461527.7 link	n.808-164C>T	intron_variant	Intron 5 of 5	1
DLEU1	ENST00000462427.2 link	n.253-35379C>T	intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes

AF:

0.740

AC:

111954

AN:

151218

Hom.:

41504

Cov.:

show subpopulations

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.:

AF XY:

0.742

AC XY:

54873

AN XY:

73952

show subpopulations

African (AFR)

AF:

0.701

AC:

28933

AN:

41274

American (AMR)

AF:

0.778

AC:

11837

AN:

15214

Ashkenazi Jewish (ASJ)

AF:

0.781

AC:

2692

AN:

3448

East Asian (EAS)

AF:

0.856

AC:

4402

AN:

5142

South Asian (SAS)

AF:

0.851

AC:

4091

AN:

4808

European-Finnish (FIN)

AF:

0.677

AC:

7111

AN:

10500

Middle Eastern (MID)

AF:

0.788

AC:

230

AN:

292

European-Non Finnish (NFE)

AF:

0.748

AC:

50644

AN:

67670

Other (OTH)

AF:

0.742

AC:

1558

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1480

2959

4439

5918

7398

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

848

1696

2544

3392

4240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.741

Hom.:

18003

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

(source)

DANN

Benign

0.43

PhyloP100

-0.23

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over