rs1717020

Positions:

• chr3-41939998-C-A
• chr3-41939998-C-G
• chr3-41939998-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.139-1801G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,652 control chromosomes in the GnomAD database, including 39,522 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 0.69 (39522 hom., cov: 29)
• Consequence: ULK4 NM_017886.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

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=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ULK4	NM_017886.4	c.139-1801G>T		intron_variant		ENST00000301831.9
ULK4	NM_001322500.2	c.139-1801G>T		intron_variant
ULK4	NM_001322501.2	c.-692-1801G>T		intron_variant
ULK4	NR_136342.2	n.275-1801G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ULK4	ENST00000301831.9	c.139-1801G>T		intron_variant		2	NM_017886.4	P1

Frequencies

GnomAD3 genomes AF: 0.693 AC: 104980 AN: 151536 Hom.: 39501 Cov.: 29

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.693 AC: 105023 AN: 151652 Hom.: 39522 Cov.: 29 AF XY: 0.694 AC XY: 51422 AN XY: 74104

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.710

Alfa AF: 0.729 Hom.: 4803

Bravo AF: 0.680

Asia WGS AF: 0.808 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.099
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: rs1717020; hg19: chr3-41981490;