Genetic Variant DLEU1:n.585+39921C>T (chr13-50545601-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 ENST00000469127.6(DLEU1):n.585+39921C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,046 control chromosomes in the GnomAD database, including 35,276 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 0.68 ( 35276 hom., cov: 31)

Consequence

DLEU1
ENST00000469127.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.749

Publications

7 publications found

Variant links:

Genes affected

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

DLEU1 links:

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

DLEU7 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000469127.6 link	n.585+39921C>T	intron_variant	Intron 5 of 6	5
DLEU1	ENST00000470726.7 link	n.346+112051C>T	intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5 link	n.458-43874C>T	intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.679

AC:

103182

AN:

151928

Hom.:

35255

Cov.:

show subpopulations

Gnomad AFR

AF:

0.621

Gnomad AMI

AF:

0.736

Gnomad AMR

AF:

0.736

Gnomad ASJ

AF:

0.708

Gnomad EAS

AF:

0.862

Gnomad SAS

AF:

0.599

Gnomad FIN

AF:

0.755

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.680

Gnomad OTH

AF:

0.669

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

GnomAD4 genome

AF:

0.679

AC:

103248

AN:

152046

Hom.:

35276

Cov.:

AF XY:

0.681

AC XY:

50598

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.621

AC:

25737

AN:

41448

American (AMR)

AF:

0.736

AC:

11242

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.708

AC:

2459

AN:

3472

East Asian (EAS)

AF:

0.862

AC:

4459

AN:

5172

South Asian (SAS)

AF:

0.599

AC:

2891

AN:

4826

European-Finnish (FIN)

AF:

0.755

AC:

7986

AN:

10582

Middle Eastern (MID)

AF:

0.616

AC:

181

AN:

294

European-Non Finnish (NFE)

AF:

0.680

AC:

46206

AN:

67964

Other (OTH)

AF:

0.673

AC:

1417

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1722

3444

5167

6889

8611

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

812

1624

2436

3248

4060

<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:

0.679

Hom.:

58637

Bravo

AF:

0.679

Asia WGS

AF:

0.726

AC:

2525

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.7

(source)

DANN

Benign

0.79

PhyloP100

-0.75

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