rs7627972

Positions:

• chr3-41438556-C-A
• chr3-41438556-C-G
• chr3-41438556-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.3492+16941G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,982 control chromosomes in the GnomAD database, including 24,889 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 0.56 (24889 hom., cov: 31)
• Consequence: ULK4 NM_017886.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655

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 = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ULK4	NM_017886.4	c.3492+16941G>T		intron_variant		ENST00000301831.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ULK4	ENST00000301831.9	c.3492+16941G>T		intron_variant		2	NM_017886.4	P1

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85082 AN: 151864 Hom.: 24853 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.560 AC: 85156 AN: 151982 Hom.: 24889 Cov.: 31 AF XY: 0.561 AC XY: 41648 AN XY: 74298

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.542

Alfa AF: 0.479 Hom.: 24437

Bravo AF: 0.565

Asia WGS AF: 0.613 AC: 2135 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	3.0
DANN	Benign	0.42

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: rs7627972; hg19: chr3-41480047;