dbSNP rs2762051: DLEU1:n.441-13353C>T (chr13-50261579-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 ENST00000461527.7(DLEU1):n.441-13353C>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 152,240 control chromosomes in the GnomAD database, including 2,067 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 ( 2067 hom., cov: 32)

Consequence

DLEU1
ENST00000461527.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

Publications

30 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=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1 link	n.443-128619C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000461527.7 link	n.441-13353C>T	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000463474.7 link	n.441-77097C>T	intron_variant	Intron 2 of 5	1
DLEU1	ENST00000468168.6 link	n.441-128619C>T	intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22872

AN:

152122

Hom.:

2060

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0724

Gnomad AMI

AF:

0.168

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.182

Gnomad EAS

AF:

0.0252

Gnomad SAS

AF:

0.0942

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.178

Gnomad NFE

AF:

0.183

Gnomad OTH

AF:

0.162

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

GnomAD4 genome

AF:

0.150

AC:

22895

AN:

152240

Hom.:

2067

Cov.:

AF XY:

0.151

AC XY:

11239

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.0724

AC:

3007

AN:

41550

American (AMR)

AF:

0.225

AC:

3443

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.182

AC:

632

AN:

3470

East Asian (EAS)

AF:

0.0248

AC:

129

AN:

5194

South Asian (SAS)

AF:

0.0944

AC:

456

AN:

4828

European-Finnish (FIN)

AF:

0.209

AC:

2219

AN:

10594

Middle Eastern (MID)

AF:

0.178

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.183

AC:

12464

AN:

67992

Other (OTH)

AF:

0.161

AC:

340

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1006

2013

3019

4026

5032

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

238

476

714

952

1190

<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:

0.172

Hom.:

11363

Bravo

AF:

0.150

Asia WGS

AF:

0.0730

AC:

255

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

0.17

(source)

DANN

Benign

0.59

PhyloP100

-1.4

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