chr3-41744517-T-C

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00

Publications

28 publications found
Variant links:
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 cancer
    Inheritance: 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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ULK4NM_017886.4 linkc.2321+9844A>G intron_variant Intron 22 of 36 ENST00000301831.9 NP_060356.2 Q96C45

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ULK4ENST00000301831.9 linkc.2321+9844A>G intron_variant Intron 22 of 36 2 NM_017886.4 ENSP00000301831.4 Q96C45

Frequencies

GnomAD3 genomes
AF:
0.315
AC:
47805
AN:
151534
Hom.:
11283
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.660
Gnomad AMI
AF:
0.214
Gnomad AMR
AF:
0.204
Gnomad ASJ
AF:
0.202
Gnomad EAS
AF:
0.168
Gnomad SAS
AF:
0.188
Gnomad FIN
AF:
0.231
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.173
Gnomad OTH
AF:
0.295
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.316
AC:
47886
AN:
151652
Hom.:
11324
Cov.:
32
AF XY:
0.315
AC XY:
23330
AN XY:
74110
show subpopulations
African (AFR)
AF:
0.661
AC:
27159
AN:
41112
American (AMR)
AF:
0.204
AC:
3115
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.202
AC:
702
AN:
3470
East Asian (EAS)
AF:
0.168
AC:
871
AN:
5182
South Asian (SAS)
AF:
0.187
AC:
903
AN:
4820
European-Finnish (FIN)
AF:
0.231
AC:
2438
AN:
10534
Middle Eastern (MID)
AF:
0.378
AC:
111
AN:
294
European-Non Finnish (NFE)
AF:
0.173
AC:
11774
AN:
67946
Other (OTH)
AF:
0.293
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:
0.223
Hom.:
17432
Bravo
AF:
0.330
Asia WGS
AF:
0.200
AC:
693
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
2.2
DANN
Benign
0.72
PhyloP100
-2.0
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs6599175; hg19: chr3-41786009; API