Variant rs11616018 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_003565.4(ULK1):c.1065C>T(p.Asp355=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 1,612,128 control chromosomes in the GnomAD database, including 497,343 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 0.66 ( 36405 hom., cov: 35)

Exomes 𝑓: 0.79 ( 460938 hom. )

Consequence

ULK1
NM_003565.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Variant links:

Genes affected

ULK1 (HGNC:12558): (unc-51 like autophagy activating kinase 1) Enables identical protein binding activity; protein serine/threonine kinase activity; and small GTPase binding activity. Involved in several processes, including autophagosome assembly; positive regulation by symbiont of host autophagy; and protein phosphorylation. Located in autophagosome; cytosol; and phagophore assembly site membrane. Is extrinsic component of autophagosome membrane; extrinsic component of omegasome membrane; and extrinsic component of phagophore assembly site membrane. Part of Atg1/ULK1 kinase complex. [provided by Alliance of Genome Resources, Apr 2022]

ULK1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP7

Synonymous conserved (PhyloP=-1.22 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ULK1	NM_003565.4 linkuse as main transcript	c.1065C>T	p.Asp355=	synonymous_variant	13/28	ENST00000321867.6
ULK1	XM_011538798.4 linkuse as main transcript	c.1065C>T	p.Asp355=	synonymous_variant	13/28
ULK1	XM_011538799.3 linkuse as main transcript	c.1065C>T	p.Asp355=	synonymous_variant	13/28
ULK1	XR_007063134.1 linkuse as main transcript	n.1445C>T		non_coding_transcript_exon_variant	13/23

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ULK1	ENST00000321867.6 linkuse as main transcript	c.1065C>T	p.Asp355=	synonymous_variant	13/28	1	NM_003565.4	P1

Frequencies

GnomAD3 genomes

AF:

0.660

AC:

100411

AN:

152102

Hom.:

36407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.367

Gnomad AMI

AF:

0.919

Gnomad AMR

AF:

0.731

Gnomad ASJ

AF:

0.760

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.690

Gnomad FIN

AF:

0.679

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.830

Gnomad OTH

AF:

0.706

GnomAD3 exomes

AF:

0.711

AC:

176460

AN:

248156

Hom.:

65779

AF XY:

0.723

AC XY:

97508

AN XY:

134816

show subpopulations

Gnomad AFR exome

AF:

0.355

Gnomad AMR exome

AF:

0.681

Gnomad ASJ exome

AF:

0.772

Gnomad EAS exome

AF:

0.354

Gnomad SAS exome

AF:

0.704

Gnomad FIN exome

AF:

0.693

Gnomad NFE exome

AF:

0.827

Gnomad OTH exome

AF:

0.766

GnomAD4 exome

AF:

0.786

AC:

1148007

AN:

1459908

Hom.:

460938

Cov.:

AF XY:

0.786

AC XY:

570652

AN XY:

726212

show subpopulations

Gnomad4 AFR exome

AF:

0.353

Gnomad4 AMR exome

AF:

0.686

Gnomad4 ASJ exome

AF:

0.767

Gnomad4 EAS exome

AF:

0.342

Gnomad4 SAS exome

AF:

0.705

Gnomad4 FIN exome

AF:

0.706

Gnomad4 NFE exome

AF:

0.832

Gnomad4 OTH exome

AF:

0.748

GnomAD4 genome

AF:

0.660

AC:

100432

AN:

152220

Hom.:

36405

Cov.:

AF XY:

0.652

AC XY:

48530

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.366

Gnomad4 AMR

AF:

0.731

Gnomad4 ASJ

AF:

0.760

Gnomad4 EAS

AF:

0.357

Gnomad4 SAS

AF:

0.690

Gnomad4 FIN

AF:

0.679

Gnomad4 NFE

AF:

0.830

Gnomad4 OTH

AF:

0.706

Alfa

AF:

0.789

Hom.:

61937

Bravo

AF:

0.650

Asia WGS

AF:

0.509

AC:

1771

AN:

3478

EpiCase

AF:

0.831

EpiControl

AF:

0.834

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

0.054

DANN

Benign

0.77

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over