rs9311275

chr3-41405135-T-Cchr3-41405135-T-G

Variant summary

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

The NM_017886.4(ULK4):c.3493-6871A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,730 control chromosomes in the GnomAD database, including 26,601 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 0.57 (26601 hom., cov: 30)
• Consequence: ULK4 NM_017886.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ULK4	NM_017886.4	c.3493-6871A>G		intron_variant		ENST00000301831.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ULK4	ENST00000301831.9	c.3493-6871A>G		intron_variant		2	NM_017886.4	P1

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87126 AN: 151610 Hom.: 26559 Cov.: 30

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.575 AC: 87206 AN: 151730 Hom.: 26601 Cov.: 30 AF XY: 0.572 AC XY: 42422 AN XY: 74124

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.561

Alfa AF: 0.367 Hom.: 978

Bravo AF: 0.584

Asia WGS AF: 0.585 AC: 2036 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	1.5
Dann	Benign	0.31

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: rs9311275; hg19: chr3-41446626;