Genetic Variant DLEU1:n.440+68184A>G (chr13-50151378-A-G) – 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+68184A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,160 control chromosomes in the GnomAD database, including 1,194 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 0.11 ( 1194 hom., cov: 32)

Consequence

DLEU1
ENST00000461527.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0470

Publications

2 publications found

Variant links:

Genes affected

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

DLEU1 links:

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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 (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1 link	n.442+68184A>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000461527.7 link	n.440+68184A>G	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000463474.7 link	n.440+68184A>G	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000468168.6 link	n.440+68184A>G	intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16183

AN:

152042

Hom.:

1186

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.0846

Gnomad ASJ

AF:

0.0591

Gnomad EAS

AF:

0.0826

Gnomad SAS

AF:

0.183

Gnomad FIN

AF:

0.0592

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0599

Gnomad OTH

AF:

0.109

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

GnomAD4 genome

AF:

0.107

AC:

16216

AN:

152160

Hom.:

1194

Cov.:

AF XY:

0.107

AC XY:

7984

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.203

AC:

8404

AN:

41464

American (AMR)

AF:

0.0845

AC:

1292

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0591

AC:

205

AN:

3468

East Asian (EAS)

AF:

0.0824

AC:

427

AN:

5180

South Asian (SAS)

AF:

0.184

AC:

887

AN:

4830

European-Finnish (FIN)

AF:

0.0592

AC:

627

AN:

10600

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0600

AC:

4077

AN:

68000

Other (OTH)

AF:

0.108

AC:

229

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

711

1423

2134

2846

3557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

376

564

752

940

<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:

0.0775

Hom.:

453

Bravo

AF:

0.112

Asia WGS

AF:

0.153

AC:

532

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

3.4

(source)

DANN

Benign

0.75

PhyloP100

0.047

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