Genetic Variant DLEU1:n.440+56751T>A (chr13-50139945-T-A) – 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.440+56751T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0391 in 152,334 control chromosomes in the GnomAD database, including 184 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 0.039 ( 184 hom., cov: 32)

Consequence

DLEU1
ENST00000461527.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.52

Publications

2 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1 link	n.442+56751T>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000461527.7 link	n.440+56751T>A	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000463474.7 link	n.440+56751T>A	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000468168.6 link	n.440+56751T>A	intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.0392

AC:

5965

AN:

152216

Hom.:

184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00924

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0442

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.000768

Gnomad SAS

AF:

0.0122

Gnomad FIN

AF:

0.0597

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0538

Gnomad OTH

AF:

0.0587

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

GnomAD4 genome

AF:

0.0391

AC:

5963

AN:

152334

Hom.:

184

Cov.:

AF XY:

0.0384

AC XY:

2859

AN XY:

74490

show subpopulations

African (AFR)

AF:

0.00921

AC:

383

AN:

41578

American (AMR)

AF:

0.0442

AC:

677

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

404

AN:

3472

East Asian (EAS)

AF:

0.000770

AC:

AN:

5194

South Asian (SAS)

AF:

0.0122

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0597

AC:

634

AN:

10620

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0537

AC:

3655

AN:

68022

Other (OTH)

AF:

0.0581

AC:

123

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

287

573

860

1146

1433

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<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:

0.0463

Hom.:

Bravo

AF:

0.0376

Asia WGS

AF:

0.00664

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

1.5

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