Variant rs1717003 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_017886.4(ULK4):c.1577+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,060 control chromosomes in the GnomAD database, including 39,433 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.69 ( 39433 hom., cov: 32)

Exomes 𝑓: 0.81 ( 422173 hom. )

Failed GnomAD Quality Control

Consequence

ULK4
NM_017886.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0970

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP6

Variant 3-41895508-C-T is Benign according to our data. Variant chr3-41895508-C-T is described in ClinVar as [Benign]. Clinvar id is 403586.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
ULK4	NM_017886.4 linkuse as main transcript	c.1577+10G>A	intron_variant	ENST00000301831.9	NP_060356.2
ULK4	NM_001322500.2 linkuse as main transcript	c.1577+10G>A	intron_variant		NP_001309429.1
ULK4	NM_001322501.2 linkuse as main transcript	c.671+10G>A	intron_variant		NP_001309430.1
ULK4	NR_136342.2 linkuse as main transcript	n.1643+10G>A	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ULK4	ENST00000301831.9 linkuse as main transcript	c.1577+10G>A		intron_variant		2	NM_017886.4	ENSP00000301831	P1
ULK4	ENST00000420927.5 linkuse as main transcript	c.1577+10G>A		intron_variant		1		ENSP00000412187

Frequencies

GnomAD3 genomes

AF:

0.689

AC:

104670

AN:

151940

Hom.:

39415

Cov.:

show subpopulations

Gnomad AFR

AF:

0.354

Gnomad AMI

AF:

0.784

Gnomad AMR

AF:

0.788

Gnomad ASJ

AF:

0.808

Gnomad EAS

AF:

0.834

Gnomad SAS

AF:

0.811

Gnomad FIN

AF:

0.776

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.829

Gnomad OTH

AF:

0.709

GnomAD3 exomes

AF:

0.769

AC:

101864

AN:

132404

Hom.:

40349

AF XY:

0.776

AC XY:

56396

AN XY:

72702

show subpopulations

Gnomad AFR exome

AF:

0.305

Gnomad AMR exome

AF:

0.832

Gnomad ASJ exome

AF:

0.806

Gnomad EAS exome

AF:

0.791

Gnomad SAS exome

AF:

0.805

Gnomad FIN exome

AF:

0.764

Gnomad NFE exome

AF:

0.803

Gnomad OTH exome

AF:

0.764

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.815

AC:

1025270

AN:

1258108

Hom.:

422173

Cov.:

AF XY:

0.816

AC XY:

510323

AN XY:

625068

show subpopulations

Gnomad4 AFR exome

AF:

0.316

Gnomad4 AMR exome

AF:

0.833

Gnomad4 ASJ exome

AF:

0.808

Gnomad4 EAS exome

AF:

0.853

Gnomad4 SAS exome

AF:

0.809

Gnomad4 FIN exome

AF:

0.782

Gnomad4 NFE exome

AF:

0.831

Gnomad4 OTH exome

AF:

0.785

GnomAD4 genome

AF:

0.689

AC:

104705

AN:

152060

Hom.:

39433

Cov.:

AF XY:

0.690

AC XY:

51280

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.353

Gnomad4 AMR

AF:

0.789

Gnomad4 ASJ

AF:

0.808

Gnomad4 EAS

AF:

0.835

Gnomad4 SAS

AF:

0.811

Gnomad4 FIN

AF:

0.776

Gnomad4 NFE

AF:

0.829

Gnomad4 OTH

AF:

0.711

Alfa

AF:

0.731

Hom.:

12601

Bravo

AF:

0.675

Asia WGS

AF:

0.804

AC:

2784

AN:

3460

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

9.4

DANN

Benign

0.83

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over