Genetic Variant DLEU1:n.585+37085G>T (chr13-50542765-G-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+37085G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,900 control chromosomes in the GnomAD database, including 2,261 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 0.15 ( 2261 hom., cov: 31)

Consequence

DLEU1
ENST00000469127.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.616

Publications

35 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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+37085G>T	intron_variant	Intron 5 of 6	5
DLEU1	ENST00000470726.7 link	n.346+109215G>T	intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5 link	n.458-46710G>T	intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22830

AN:

151780

Hom.:

2262

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0352

Gnomad AMI

AF:

0.291

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.178

Gnomad EAS

AF:

0.0193

Gnomad SAS

AF:

0.0874

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.154

Gnomad NFE

AF:

0.211

Gnomad OTH

AF:

0.172

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

GnomAD4 genome

AF:

0.150

AC:

22816

AN:

151900

Hom.:

2261

Cov.:

AF XY:

0.151

AC XY:

11185

AN XY:

74220

show subpopulations

African (AFR)

AF:

0.0351

AC:

1453

AN:

41448

American (AMR)

AF:

0.153

AC:

2327

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.178

AC:

616

AN:

3466

East Asian (EAS)

AF:

0.0194

AC:

100

AN:

5160

South Asian (SAS)

AF:

0.0864

AC:

415

AN:

4802

European-Finnish (FIN)

AF:

0.274

AC:

2885

AN:

10538

Middle Eastern (MID)

AF:

0.154

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.211

AC:

14354

AN:

67948

Other (OTH)

AF:

0.169

AC:

356

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.534

Heterozygous variant carriers

925

1849

2774

3698

4623

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

244

488

732

976

1220

<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:

0.190

Hom.:

10578

Bravo

AF:

0.139

Asia WGS

AF:

0.0500

AC:

178

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.57

(source)

DANN

Benign

0.51

PhyloP100

-0.62

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