rs1495696

Positions:

• chr3-41490873-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

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 (HGNC:):

ACMG classification

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
ULK4	NM_017886.4	c.3227-27620T>G		intron_variant		ENST00000301831.9	NP_060356.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ULK4	ENST00000301831.9	c.3227-27620T>G		intron_variant		2	NM_017886.4	ENSP00000301831.4

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62387 AN: 151866 Hom.: 12989 Cov.: 32

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

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

Other links and lift over

dbSNP: rs1495696; hg19: chr3-41532364;