dbSNP rs3118906: DLEU1:n.363-541G>A (chr13-50532652-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000460525.6(DLEU1):n.363-541G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,838 control chromosomes in the GnomAD database, including 3,947 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 0.21 ( 3947 hom., cov: 32)

Consequence

DLEU1
ENST00000460525.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.259

Publications

28 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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 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	ENST00000460525.6 link	n.363-541G>A	intron_variant	Intron 3 of 3	1
DLEU1	ENST00000462427.2 link	n.452-541G>A	intron_variant	Intron 3 of 3	1
DLEU1	ENST00000469127.6 link	n.585+26972G>A	intron_variant	Intron 5 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31844

AN:

151718

Hom.:

3947

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.203

Gnomad ASJ

AF:

0.270

Gnomad EAS

AF:

0.0197

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.237

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

GnomAD4 genome

AF:

0.210

AC:

31846

AN:

151838

Hom.:

3947

Cov.:

AF XY:

0.208

AC XY:

15456

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.101

AC:

4183

AN:

41488

American (AMR)

AF:

0.203

AC:

3101

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.270

AC:

937

AN:

3466

East Asian (EAS)

AF:

0.0197

AC:

102

AN:

5178

South Asian (SAS)

AF:

0.124

AC:

599

AN:

4826

European-Finnish (FIN)

AF:

0.332

AC:

3502

AN:

10558

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.274

AC:

18537

AN:

67740

Other (OTH)

AF:

0.234

AC:

495

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1234

2468

3701

4935

6169

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<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:

0.252

Hom.:

15656

Bravo

AF:

0.198

Asia WGS

AF:

0.0720

AC:

253

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.3

(source)

DANN

Benign

0.71

PhyloP100

-0.26

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