dbSNP rs2476391: DLEU2:n.794A>G (chr13-50044368-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 ENST00000433070.9(DLEU2):n.794A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0523 in 152,066 control chromosomes in the GnomAD database, including 333 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 0.052 ( 333 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

DLEU2
ENST00000433070.9 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.72

Publications

3 publications found

Variant links:

Genes affected

DLEU2 (HGNC:13748): (deleted in lymphocytic leukemia 2) This locus represents a microRNA host gene and also produces long alternatively spliced non-coding RNAs. This genome region was observed to be deleted or epigenetically suppressed in leukemia, and was implicated as a negative regulator of cell proliferation. However, an alternative transcript produced at this locus was also found to promote progression through the cell cycle via angiotensin I converting enzyme 2 and cyclin D1. [provided by RefSeq, Dec 2017]

DLEU2 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=-0.55).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
DLEU2	NR_152567.1 link	n.861A>G	non_coding_transcript_exon_variant	Exon 5 of 5
DLEU2	NR_152568.1 link	n.766A>G	non_coding_transcript_exon_variant	Exon 4 of 4
DLEU2	NR_152566.1 link	n.899+272A>G	intron_variant	Intron 8 of 13

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DLEU2	ENST00000433070.9 link	n.794A>G	non_coding_transcript_exon_variant	Exon 4 of 4	1
DLEU2	ENST00000425586.6 link	n.778+283A>G	intron_variant	Intron 5 of 6	1
DLEU2	ENST00000621282.4 link	n.899+272A>G	intron_variant	Intron 8 of 13	1

Frequencies

GnomAD3 genomes

AF:

0.0524

AC:

7956

AN:

151948

Hom.:

331

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.0660

Gnomad ASJ

AF:

0.0590

Gnomad EAS

AF:

0.0817

Gnomad SAS

AF:

0.183

Gnomad FIN

AF:

0.0582

Gnomad MID

AF:

0.0828

Gnomad NFE

AF:

0.0607

Gnomad OTH

AF:

0.0670

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.0523

AC:

7955

AN:

152066

Hom.:

333

Cov.:

AF XY:

0.0551

AC XY:

4093

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.0119

AC:

493

AN:

41562

American (AMR)

AF:

0.0659

AC:

1007

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0590

AC:

205

AN:

3472

East Asian (EAS)

AF:

0.0815

AC:

423

AN:

5188

South Asian (SAS)

AF:

0.183

AC:

886

AN:

4832

European-Finnish (FIN)

AF:

0.0582

AC:

615

AN:

10566

Middle Eastern (MID)

AF:

0.0822

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0608

AC:

4123

AN:

67854

Other (OTH)

AF:

0.0664

AC:

140

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

380

760

1141

1521

1901

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

220

330

440

550

<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:

0.0526

Hom.:

Bravo

AF:

0.0485

Asia WGS

AF:

0.135

AC:

461

AN:

3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

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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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