Genetic Variant DLEU1:n.556-3107T>C (chr13-50411982-T-C) – 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.556-3107T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,144 control chromosomes in the GnomAD database, including 35,922 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 0.68 ( 35922 hom., cov: 33)

Consequence

DLEU1
ENST00000461527.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.127

Publications

9 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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1 link	n.537-21431T>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU1	ENST00000461527.7 link	n.556-3107T>C	intron_variant	Intron 3 of 5	1
DLEU1	ENST00000463474.7 link	n.600-21431T>C	intron_variant	Intron 3 of 5	1
DLEU1	ENST00000468168.6 link	n.535-21431T>C	intron_variant	Intron 3 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.678

AC:

102999

AN:

152026

Hom.:

35910

Cov.:

show subpopulations

Gnomad AFR

AF:

0.588

Gnomad AMI

AF:

0.727

Gnomad AMR

AF:

0.739

Gnomad ASJ

AF:

0.739

Gnomad EAS

AF:

0.210

Gnomad SAS

AF:

0.601

Gnomad FIN

AF:

0.779

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.739

Gnomad OTH

AF:

0.691

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

GnomAD4 genome

AF:

0.677

AC:

103041

AN:

152144

Hom.:

35922

Cov.:

AF XY:

0.676

AC XY:

50265

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.588

AC:

24373

AN:

41482

American (AMR)

AF:

0.739

AC:

11296

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.739

AC:

2564

AN:

3470

East Asian (EAS)

AF:

0.209

AC:

1086

AN:

5188

South Asian (SAS)

AF:

0.601

AC:

2890

AN:

4812

European-Finnish (FIN)

AF:

0.779

AC:

8265

AN:

10606

Middle Eastern (MID)

AF:

0.718

AC:

211

AN:

294

European-Non Finnish (NFE)

AF:

0.739

AC:

50250

AN:

67988

Other (OTH)

AF:

0.684

AC:

1443

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1614

3229

4843

6458

8072

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

798

1596

2394

3192

3990

<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:

0.707

Hom.:

80890

Bravo

AF:

0.668

Asia WGS

AF:

0.461

AC:

1604

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.9

(source)

DANN

Benign

0.64

PhyloP100

-0.13

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