Variant chr3-41566050-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_017886.4(ULK4):c.3201G>A(p.Ser1067=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00554 in 1,613,564 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0037 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0057 ( 33 hom. )

Consequence

ULK4
NM_017886.4 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.83

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BP6

Variant 3-41566050-C-T is Benign according to our data. Variant chr3-41566050-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 789277.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.83 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 33 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ULK4	NM_017886.4 linkuse as main transcript	c.3201G>A	p.Ser1067=	synonymous_variant	32/37	ENST00000301831.9	NP_060356.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ULK4	ENST00000301831.9 linkuse as main transcript	c.3201G>A	p.Ser1067=	synonymous_variant	32/37	2	NM_017886.4	ENSP00000301831	P1

Frequencies

GnomAD3 genomes

AF:

0.00371

AC:

564

AN:

151922

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00171

Gnomad ASJ

AF:

0.0101

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00187

Gnomad FIN

AF:

0.000663

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00641

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00445

AC:

1109

AN:

249194

Hom.:

AF XY:

0.00473

AC XY:

640

AN XY:

135206

show subpopulations

Gnomad AFR exome

AF:

0.000969

Gnomad AMR exome

AF:

0.00180

Gnomad ASJ exome

AF:

0.0118

Gnomad EAS exome

AF:

0.0000557

Gnomad SAS exome

AF:

0.00173

Gnomad FIN exome

AF:

0.00125

Gnomad NFE exome

AF:

0.00712

Gnomad OTH exome

AF:

0.00448

GnomAD4 exome

AF:

0.00573

AC:

8376

AN:

1461524

Hom.:

Cov.:

AF XY:

0.00574

AC XY:

4176

AN XY:

727050

show subpopulations

Gnomad4 AFR exome

AF:

0.000896

Gnomad4 AMR exome

AF:

0.00195

Gnomad4 ASJ exome

AF:

0.0116

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00160

Gnomad4 FIN exome

AF:

0.00107

Gnomad4 NFE exome

AF:

0.00671

Gnomad4 OTH exome

AF:

0.00475

GnomAD4 genome

AF:

0.00370

AC:

563

AN:

152040

Hom.:

Cov.:

AF XY:

0.00334

AC XY:

248

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.00104

Gnomad4 AMR

AF:

0.00170

Gnomad4 ASJ

AF:

0.0101

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.000663

Gnomad4 NFE

AF:

0.00640

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00536

Hom.:

Bravo

AF:

0.00404

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2023	ULK4: BP4, BP7, BS2 -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 23, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

7.3

DANN

Benign

0.56

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over