Genetic Variant DLEU1:n.585+38633G>A (chr13-50544313-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000469127.6(DLEU1):n.585+38633G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 152,106 control chromosomes in the GnomAD database, including 432 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 0.069 ( 432 hom., cov: 32)

Consequence

DLEU1
ENST00000469127.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.70

Publications

1 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0852 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+38633G>A	intron_variant	Intron 5 of 6	5
DLEU1	ENST00000470726.7 link	n.346+110763G>A	intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5 link	n.458-45162G>A	intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.0694

AC:

10548

AN:

151986

Hom.:

431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0574

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0498

Gnomad ASJ

AF:

0.0956

Gnomad EAS

AF:

0.0187

Gnomad SAS

AF:

0.0914

Gnomad FIN

AF:

0.0701

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0826

Gnomad OTH

AF:

0.0737

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

GnomAD4 genome

AF:

0.0695

AC:

10565

AN:

152106

Hom.:

432

Cov.:

AF XY:

0.0689

AC XY:

5124

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.0572

AC:

2372

AN:

41492

American (AMR)

AF:

0.0498

AC:

760

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0956

AC:

332

AN:

3472

East Asian (EAS)

AF:

0.0191

AC:

AN:

5182

South Asian (SAS)

AF:

0.0923

AC:

444

AN:

4810

European-Finnish (FIN)

AF:

0.0701

AC:

741

AN:

10570

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0826

AC:

5616

AN:

67988

Other (OTH)

AF:

0.0799

AC:

169

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

493

986

1478

1971

2464

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0820

Hom.:

456

Bravo

AF:

0.0663

Asia WGS

AF:

0.0910

AC:

316

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

1.7

Splicing

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

Publications

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chr13-50544313-G-A

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