Genetic Variant DLEU1:n.555+10808C>T (chr13-50285854-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 ENST00000461527.7(DLEU1):n.555+10808C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,888 control chromosomes in the GnomAD database, including 13,957 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 0.41 ( 13957 hom., cov: 31)

Consequence

DLEU1
ENST00000461527.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.306

Publications

8 publications found

Variant links:

Genes affected

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

DLEU1 links:

Genome browser will be placed here

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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1 link	n.443-104344C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000461527.7 link	n.555+10808C>T	intron_variant	Intron 3 of 5	1
DLEU1	ENST00000463474.7 link	n.441-52822C>T	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000468168.6 link	n.441-104344C>T	intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.414

AC:

62844

AN:

151770

Hom.:

13968

Cov.:

show subpopulations

Gnomad AFR

AF:

0.280

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.510

Gnomad EAS

AF:

0.751

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.487

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.472

Gnomad OTH

AF:

0.432

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

GnomAD4 genome

AF:

0.414

AC:

62835

AN:

151888

Hom.:

13957

Cov.:

AF XY:

0.412

AC XY:

30571

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.280

AC:

11594

AN:

41426

American (AMR)

AF:

0.337

AC:

5136

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.510

AC:

1771

AN:

3470

East Asian (EAS)

AF:

0.751

AC:

3883

AN:

5168

South Asian (SAS)

AF:

0.376

AC:

1812

AN:

4818

European-Finnish (FIN)

AF:

0.487

AC:

5124

AN:

10526

Middle Eastern (MID)

AF:

0.449

AC:

131

AN:

292

European-Non Finnish (NFE)

AF:

0.472

AC:

32089

AN:

67914

Other (OTH)

AF:

0.430

AC:

907

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1765

3530

5295

7060

8825

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

592

1184

1776

2368

2960

<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:

0.455

Hom.:

11602

Bravo

AF:

0.403

Asia WGS

AF:

0.489

AC:

1699

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.5

(source)

DANN

Benign

0.73

PhyloP100

-0.31

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