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rs11129896

Variant summary

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

The NM_017886.4(ULK4):c.3679-4702A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,062 control chromosomes in the GnomAD database, including 10,273 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 0.34 ( 10273 hom., cov: 32)

Consequence

ULK4
NM_017886.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.08
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]
CTNNB1 (HGNC:2514): (catenin beta 1) The protein encoded by this gene is part of a complex of proteins that constitute adherens junctions (AJs). AJs are necessary for the creation and maintenance of epithelial cell layers by regulating cell growth and adhesion between cells. The encoded protein also anchors the actin cytoskeleton and may be responsible for transmitting the contact inhibition signal that causes cells to stop dividing once the epithelial sheet is complete. Finally, this protein binds to the product of the APC gene, which is mutated in adenomatous polyposis of the colon. Mutations in this gene are a cause of colorectal cancer (CRC), pilomatrixoma (PTR), medulloblastoma (MDB), and ovarian cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ULK4NM_017886.4 linkuse as main transcriptc.3679-4702A>G intron_variant ENST00000301831.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ULK4ENST00000301831.9 linkuse as main transcriptc.3679-4702A>G intron_variant 2 NM_017886.4 P1
ULK4ENST00000489118.1 linkuse as main transcriptn.347-3152A>G intron_variant, non_coding_transcript_variant 1
CTNNB1ENST00000471014.2 linkuse as main transcriptc.*13-4056T>C intron_variant, NMD_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.338
AC:
51417
AN:
151944
Hom.:
10274
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.418
Gnomad AMR
AF:
0.410
Gnomad ASJ
AF:
0.426
Gnomad EAS
AF:
0.211
Gnomad SAS
AF:
0.383
Gnomad FIN
AF:
0.427
Gnomad MID
AF:
0.335
Gnomad NFE
AF:
0.440
Gnomad OTH
AF:
0.349
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.338
AC:
51417
AN:
152062
Hom.:
10273
Cov.:
32
AF XY:
0.338
AC XY:
25101
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.123
Gnomad4 AMR
AF:
0.411
Gnomad4 ASJ
AF:
0.426
Gnomad4 EAS
AF:
0.212
Gnomad4 SAS
AF:
0.383
Gnomad4 FIN
AF:
0.427
Gnomad4 NFE
AF:
0.440
Gnomad4 OTH
AF:
0.346
Alfa
AF:
0.421
Hom.:
20302
Bravo
AF:
0.329
Asia WGS
AF:
0.331
AC:
1156
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
Cadd
Benign
0.058
Dann
Benign
0.57

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: rs11129896; hg19: chr3-41295767; API