dbSNP rs1928123: DLEU1:n.585+40029A>C (chr13-50545709-A-C) – 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+40029A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,144 control chromosomes in the GnomAD database, including 1,789 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 0.14 ( 1789 hom., cov: 32)

Consequence

DLEU1
ENST00000469127.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0350

Publications

5 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 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+40029A>C	intron_variant	Intron 5 of 6	5
DLEU1	ENST00000470726.7 link	n.346+112159A>C	intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5 link	n.458-43766A>C	intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

21903

AN:

152026

Hom.:

1775

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.0373

Gnomad AMR

AF:

0.214

Gnomad ASJ

AF:

0.0948

Gnomad EAS

AF:

0.0696

Gnomad SAS

AF:

0.0959

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.129

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

GnomAD4 genome

AF:

0.144

AC:

21952

AN:

152144

Hom.:

1789

Cov.:

AF XY:

0.146

AC XY:

10870

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.156

AC:

6476

AN:

41498

American (AMR)

AF:

0.215

AC:

3284

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0948

AC:

329

AN:

3472

East Asian (EAS)

AF:

0.0688

AC:

356

AN:

5176

South Asian (SAS)

AF:

0.0959

AC:

463

AN:

4826

European-Finnish (FIN)

AF:

0.213

AC:

2256

AN:

10584

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.124

AC:

8463

AN:

67986

Other (OTH)

AF:

0.127

AC:

269

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

931

1862

2794

3725

4656

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.123

Hom.:

1577

Bravo

AF:

0.147

Asia WGS

AF:

0.100

AC:

349

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.4

(source)

DANN

Benign

0.69

PhyloP100

0.035

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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