GeneBe

ENST00000461527.7:n.555+10808C>T

Variant names:

Variant summary

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

The ENST00000461527.7(DLEU1):​n.555+10808C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,888 control chromosomes in the GnomAD database, including 13,957 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 0.41 ( 13957 hom., cov: 31)

Consequence

DLEU1
ENST00000461527.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.306

Publications

8 publications found
Variant links:
Genes affected
DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)

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=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DLEU1NR_109974.1 linkn.443-104344C>T intron_variant Intron 2 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DLEU1ENST00000461527.7 linkn.555+10808C>T intron_variant Intron 3 of 5 1
DLEU1ENST00000463474.7 linkn.441-52822C>T intron_variant Intron 2 of 5 1
DLEU1ENST00000468168.6 linkn.441-104344C>T intron_variant Intron 2 of 5 1

Frequencies

GnomAD3 genomes
AF:
0.414
AC:
62844
AN:
151770
Hom.:
13968
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.280
Gnomad AMI
AF:
0.426
Gnomad AMR
AF:
0.337
Gnomad ASJ
AF:
0.510
Gnomad EAS
AF:
0.751
Gnomad SAS
AF:
0.378
Gnomad FIN
AF:
0.487
Gnomad MID
AF:
0.449
Gnomad NFE
AF:
0.472
Gnomad OTH
AF:
0.432
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.414
AC:
62835
AN:
151888
Hom.:
13957
Cov.:
31
AF XY:
0.412
AC XY:
30571
AN XY:
74248
show subpopulations
African (AFR)
AF:
0.280
AC:
11594
AN:
41426
American (AMR)
AF:
0.337
AC:
5136
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
0.510
AC:
1771
AN:
3470
East Asian (EAS)
AF:
0.751
AC:
3883
AN:
5168
South Asian (SAS)
AF:
0.376
AC:
1812
AN:
4818
European-Finnish (FIN)
AF:
0.487
AC:
5124
AN:
10526
Middle Eastern (MID)
AF:
0.449
AC:
131
AN:
292
European-Non Finnish (NFE)
AF:
0.472
AC:
32089
AN:
67914
Other (OTH)
AF:
0.430
AC:
907
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1765
3530
5295
7060
8825
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
592
1184
1776
2368
2960
<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:
0.455
Hom.:
11602
Bravo
AF:
0.403
Asia WGS
AF:
0.489
AC:
1699
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
2.5
DANN
Benign
0.73
PhyloP100
-0.31

Splicing

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

Publications

Other links and lift over

dbSNP: rs806349; hg19: chr13-50859990; API