rs900569

Positions:

• chr3-41818481-C-T

Variant summary

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

The NM_017886.4(ULK4):​c.1848+942G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,162 control chromosomes in the GnomAD database, including 31,932 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 0.62 (31932 hom., cov: 33)
• Consequence: ULK4 NM_017886.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ULK4	NM_017886.4	c.1848+942G>A		intron_variant		ENST00000301831.9	NP_060356.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ULK4	ENST00000301831.9	c.1848+942G>A		intron_variant		2	NM_017886.4	ENSP00000301831	P1
ULK4	ENST00000460406.1	n.329+942G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94445 AN: 152044 Hom.: 31864 Cov.: 33

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.607

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.621 AC: 94568 AN: 152162 Hom.: 31932 Cov.: 33 AF XY: 0.618 AC XY: 45985 AN XY: 74392

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.604

Alfa AF: 0.530 Hom.: 29931

Bravo AF: 0.648

Asia WGS AF: 0.533 AC: 1858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0060
DANN	Benign	0.41

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: rs900569; hg19: chr3-41859973;