rs1795355

Variant names:

• chr3-41558035-T-C
• rs1795355
• NM_017886.4:c.3226+7990A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017886.4(ULK4):​c.3226+7990A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 152,006 control chromosomes in the GnomAD database, including 15,539 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 0.43 (15539 hom., cov: 32)
• Consequence: ULK4 NM_017886.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• prostate cancer

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017886.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ULK4	NM_017886.4	MANE Select	c.3226+7990A>G		intron	N/A	NP_060356.2
	ULK4	NM_001322500.2		c.3226+7990A>G		intron	N/A	NP_001309429.1
	ULK4	NM_001322501.2		c.2320+7990A>G		intron	N/A	NP_001309430.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ULK4	ENST00000301831.9	TSL:2 MANE Select	c.3226+7990A>G		intron	N/A	ENSP00000301831.4

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65938 AN: 151888 Hom.: 15521 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.434 AC: 65980 AN: 152006 Hom.: 15539 Cov.: 32 AF XY: 0.437 AC XY: 32432 AN XY: 74268

African (AFR) AF: 0.239 AC: 9905 AN: 41498

American (AMR) AF: 0.517 AC: 7897 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1927 AN: 3472

East Asian (EAS) AF: 0.378 AC: 1953 AN: 5166

South Asian (SAS) AF: 0.450 AC: 2165 AN: 4816

European-Finnish (FIN) AF: 0.512 AC: 5379 AN: 10504

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35194 AN: 67956

Other (OTH) AF: 0.456 AC: 963 AN: 2112

Alfa AF: 0.488 Hom.: 52046

Bravo AF: 0.426

Asia WGS AF: 0.384 AC: 1335 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.62
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1795355; hg19: chr3-41599526;