chr3-41744517-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017886.4(ULK4):c.2321+9844A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,652 control chromosomes in the GnomAD database, including 11,324 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 0.32 ( 11324 hom., cov: 32)
Consequence
ULK4
NM_017886.4 intron
NM_017886.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.00
Publications
28 publications found
Genes affected
ULK4 (HGNC:15784): (unc-51 like kinase 4) This gene encodes a member of the unc-51-like serine/threonine kinase (STK) family. Members of this protein family play a role in neuronal growth and endocytosis. The encoded protein is likely involved in neurite branching, neurite elongation and neuronal migration. Genome-wide association studies (GWAS) indicate an association of variations in this gene with blood pressure and hypertension. Sequence variations in this gene may also be be associated with psychiatric disorders, including schizophrenia and bipolar disorder. Pseudogenes associated with this gene have been identified and are located on chromosome 15. [provided by RefSeq, Jul 2016]
ULK4 Gene-Disease associations (from GenCC):
- prostate cancerInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.315 AC: 47805AN: 151534Hom.: 11283 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
47805
AN:
151534
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: 0.316 AC: 47886AN: 151652Hom.: 11324 Cov.: 32 AF XY: 0.315 AC XY: 23330AN XY: 74110 show subpopulations
GnomAD4 genome
AF:
AC:
47886
AN:
151652
Hom.:
Cov.:
32
AF XY:
AC XY:
23330
AN XY:
74110
show subpopulations
African (AFR)
AF:
AC:
27159
AN:
41112
American (AMR)
AF:
AC:
3115
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
702
AN:
3470
East Asian (EAS)
AF:
AC:
871
AN:
5182
South Asian (SAS)
AF:
AC:
903
AN:
4820
European-Finnish (FIN)
AF:
AC:
2438
AN:
10534
Middle Eastern (MID)
AF:
AC:
111
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11774
AN:
67946
Other (OTH)
AF:
AC:
618
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1301
2602
3904
5205
6506
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
426
852
1278
1704
2130
<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:
693
AN:
3476
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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