chr11-24715070-T-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001009909.4(LUZP2):c.63-14099T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,070 control chromosomes in the GnomAD database, including 4,280 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 0.19 ( 4280 hom., cov: 32)
Consequence
LUZP2
NM_001009909.4 intron
NM_001009909.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.307
Publications
1 publications found
Genes affected
LUZP2 (HGNC:23206): (leucine zipper protein 2) This gene encodes a leucine zipper protein. This protein is deleted in some patients with Wilms tumor-Aniridia-Genitourinary anomalies-mental Retardation (WAGR) syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2011]
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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=-0.76).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.192 AC: 29137AN: 151952Hom.: 4262 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
29137
AN:
151952
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.192 AC: 29199AN: 152070Hom.: 4280 Cov.: 32 AF XY: 0.194 AC XY: 14392AN XY: 74346 show subpopulations
GnomAD4 genome
AF:
AC:
29199
AN:
152070
Hom.:
Cov.:
32
AF XY:
AC XY:
14392
AN XY:
74346
show subpopulations
African (AFR)
AF:
AC:
16058
AN:
41416
American (AMR)
AF:
AC:
3622
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
216
AN:
3470
East Asian (EAS)
AF:
AC:
759
AN:
5160
South Asian (SAS)
AF:
AC:
1227
AN:
4818
European-Finnish (FIN)
AF:
AC:
638
AN:
10612
Middle Eastern (MID)
AF:
AC:
36
AN:
294
European-Non Finnish (NFE)
AF:
AC:
6253
AN:
68006
Other (OTH)
AF:
AC:
332
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1082
2163
3245
4326
5408
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
284
568
852
1136
1420
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
759
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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