GeneBe

ENST00000469127.6:n.585+31539T>G

Variant names:

Variant summary

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

The ENST00000469127.6(DLEU1):​n.585+31539T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,220 control chromosomes in the GnomAD database, including 2,270 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 0.15 ( 2270 hom., cov: 32)

Consequence

DLEU1
ENST00000469127.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.491

Publications

40 publications found
Variant links:
Genes affected
DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)
DLEU7 (HGNC:17567): (deleted in lymphocytic leukemia 7)

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 (NFE) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DLEU1ENST00000469127.6 linkn.585+31539T>G intron_variant Intron 5 of 6 5
DLEU1ENST00000470726.7 linkn.346+103669T>G intron_variant Intron 3 of 5 5
DLEU1ENST00000479420.5 linkn.457+44458T>G intron_variant Intron 4 of 5 5

Frequencies

GnomAD3 genomes
AF:
0.151
AC:
22945
AN:
152102
Hom.:
2271
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0371
Gnomad AMI
AF:
0.291
Gnomad AMR
AF:
0.153
Gnomad ASJ
AF:
0.178
Gnomad EAS
AF:
0.0194
Gnomad SAS
AF:
0.0864
Gnomad FIN
AF:
0.274
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.211
Gnomad OTH
AF:
0.173
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.151
AC:
22931
AN:
152220
Hom.:
2270
Cov.:
32
AF XY:
0.151
AC XY:
11241
AN XY:
74416
show subpopulations
African (AFR)
AF:
0.0370
AC:
1537
AN:
41552
American (AMR)
AF:
0.153
AC:
2336
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.178
AC:
617
AN:
3470
East Asian (EAS)
AF:
0.0195
AC:
101
AN:
5184
South Asian (SAS)
AF:
0.0854
AC:
412
AN:
4822
European-Finnish (FIN)
AF:
0.274
AC:
2895
AN:
10582
Middle Eastern (MID)
AF:
0.160
AC:
47
AN:
294
European-Non Finnish (NFE)
AF:
0.211
AC:
14362
AN:
67996
Other (OTH)
AF:
0.170
AC:
359
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
952
1904
2856
3808
4760
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
246
492
738
984
1230
<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:
0.186
Hom.:
10702
Bravo
AF:
0.140
Asia WGS
AF:
0.0500
AC:
178
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
2.2
DANN
Benign
0.82
PhyloP100
-0.49
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs3116602; hg19: chr13-51111355; API