Genetic Variant DLEU1:n.441-7745C>T (chr13-50267187-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.441-7745C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,846 control chromosomes in the GnomAD database, including 17,659 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 0.47 ( 17659 hom., cov: 31)

Consequence

DLEU1
ENST00000461527.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0160

Publications

28 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1 link	n.443-123011C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000461527.7 link	n.441-7745C>T	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000463474.7 link	n.441-71489C>T	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000468168.6 link	n.441-123011C>T	intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.471

AC:

71501

AN:

151728

Hom.:

17669

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.381

Gnomad AMR

AF:

0.394

Gnomad ASJ

AF:

0.536

Gnomad EAS

AF:

0.732

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.593

Gnomad MID

AF:

0.455

Gnomad NFE

AF:

0.525

Gnomad OTH

AF:

0.492

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

GnomAD4 genome

AF:

0.471

AC:

71488

AN:

151846

Hom.:

17659

Cov.:

AF XY:

0.470

AC XY:

34900

AN XY:

74182

show subpopulations

African (AFR)

AF:

0.349

AC:

14442

AN:

41416

American (AMR)

AF:

0.394

AC:

6009

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.536

AC:

1855

AN:

3464

East Asian (EAS)

AF:

0.733

AC:

3778

AN:

5156

South Asian (SAS)

AF:

0.411

AC:

1975

AN:

4800

European-Finnish (FIN)

AF:

0.593

AC:

6253

AN:

10536

Middle Eastern (MID)

AF:

0.462

AC:

135

AN:

292

European-Non Finnish (NFE)

AF:

0.525

AC:

35666

AN:

67904

Other (OTH)

AF:

0.488

AC:

1028

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1832

3664

5496

7328

9160

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

652

1304

1956

2608

3260

<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:

0.513

Hom.:

87108

Bravo

AF:

0.457

Asia WGS

AF:

0.490

AC:

1703

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.4

(source)

DANN

Benign

0.71

PhyloP100

0.016

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