rs1495696

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017886.4(ULK4):​c.3227-27620T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,982 control chromosomes in the GnomAD database, including 12,993 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 ( 12993 hom., cov: 32)

Consequence

ULK4
NM_017886.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.389
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ULK4NM_017886.4 linkuse as main transcriptc.3227-27620T>G intron_variant ENST00000301831.9 NP_060356.2 Q96C45

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ULK4ENST00000301831.9 linkuse as main transcriptc.3227-27620T>G intron_variant 2 NM_017886.4 ENSP00000301831.4 Q96C45

Frequencies

GnomAD3 genomes
AF:
0.411
AC:
62387
AN:
151866
Hom.:
12989
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.437
Gnomad AMI
AF:
0.411
Gnomad AMR
AF:
0.389
Gnomad ASJ
AF:
0.432
Gnomad EAS
AF:
0.163
Gnomad SAS
AF:
0.393
Gnomad FIN
AF:
0.385
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.423
Gnomad OTH
AF:
0.423
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.411
AC:
62409
AN:
151982
Hom.:
12993
Cov.:
32
AF XY:
0.404
AC XY:
30012
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.437
Gnomad4 AMR
AF:
0.388
Gnomad4 ASJ
AF:
0.432
Gnomad4 EAS
AF:
0.163
Gnomad4 SAS
AF:
0.392
Gnomad4 FIN
AF:
0.385
Gnomad4 NFE
AF:
0.423
Gnomad4 OTH
AF:
0.421
Alfa
AF:
0.327
Hom.:
1563
Bravo
AF:
0.410
Asia WGS
AF:
0.317
AC:
1104
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.0
DANN
Benign
0.52

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1495696; hg19: chr3-41532364; API