dbSNP rs7991818: DLEU1:n.688-2225C>T (chr13-50636244-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.688-2225C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,986 control chromosomes in the GnomAD database, including 2,559 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 0.16 ( 2559 hom., cov: 31)

Consequence

DLEU1
ENST00000469127.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0120

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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 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.688-2225C>T	intron_variant	Intron 6 of 6	5
DLEU1	ENST00000470726.7 link	n.347-83403C>T	intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5 link	n.560-12346C>T	intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24709

AN:

151868

Hom.:

2555

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0431

Gnomad AMI

AF:

0.251

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.0718

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.185

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

GnomAD4 genome

AF:

0.163

AC:

24718

AN:

151986

Hom.:

2559

Cov.:

AF XY:

0.164

AC XY:

12156

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.0433

AC:

1798

AN:

41504

American (AMR)

AF:

0.157

AC:

2394

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

602

AN:

3472

East Asian (EAS)

AF:

0.132

AC:

681

AN:

5150

South Asian (SAS)

AF:

0.0708

AC:

341

AN:

4818

European-Finnish (FIN)

AF:

0.296

AC:

3122

AN:

10550

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.223

AC:

15127

AN:

67912

Other (OTH)

AF:

0.183

AC:

387

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

987

1974

2962

3949

4936

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.201

Hom.:

10359

Bravo

AF:

0.153

Asia WGS

AF:

0.0750

AC:

264

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.3

(source)

DANN

Benign

0.56

PhyloP100

-0.012

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