Variant 12-131914520-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000321867.6(ULK1):c.1373+43T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 1,588,298 control chromosomes in the GnomAD database, including 95,901 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 0.26 ( 6463 hom., cov: 35)

Exomes 𝑓: 0.35 ( 89438 hom. )

Consequence

ULK1
ENST00000321867.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.70

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:

ULK1 (HGNC:):

ULK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
ULK1	NM_003565.4 linkuse as main transcript	c.1373+43T>G	intron_variant	ENST00000321867.6	NP_003556.2	O75385
ULK1	XM_011538798.4 linkuse as main transcript	c.1373+43T>G	intron_variant		XP_011537100.1
ULK1	XM_011538799.3 linkuse as main transcript	c.1373+43T>G	intron_variant		XP_011537101.1
ULK1	XR_007063134.1 linkuse as main transcript	n.1753+43T>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ULK1	ENST00000321867.6 linkuse as main transcript	c.1373+43T>G		intron_variant		1	NM_003565.4	ENSP00000324560.3		O75385

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39649

AN:

152034

Hom.:

6469

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0644

Gnomad AMI

AF:

0.248

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.332

Gnomad EAS

AF:

0.212

Gnomad SAS

AF:

0.269

Gnomad FIN

AF:

0.313

Gnomad MID

AF:

0.398

Gnomad NFE

AF:

0.371

Gnomad OTH

AF:

0.263

GnomAD3 exomes

AF:

0.299

AC:

65701

AN:

219888

Hom.:

10451

AF XY:

0.307

AC XY:

36862

AN XY:

120014

show subpopulations

Gnomad AFR exome

AF:

0.0583

Gnomad AMR exome

AF:

0.228

Gnomad ASJ exome

AF:

0.328

Gnomad EAS exome

AF:

0.216

Gnomad SAS exome

AF:

0.272

Gnomad FIN exome

AF:

0.324

Gnomad NFE exome

AF:

0.372

Gnomad OTH exome

AF:

0.316

GnomAD4 exome

AF:

0.347

AC:

498855

AN:

1436146

Hom.:

89438

Cov.:

AF XY:

0.347

AC XY:

246464

AN XY:

711240

show subpopulations

Gnomad4 AFR exome

AF:

0.0548

Gnomad4 AMR exome

AF:

0.231

Gnomad4 ASJ exome

AF:

0.326

Gnomad4 EAS exome

AF:

0.226

Gnomad4 SAS exome

AF:

0.276

Gnomad4 FIN exome

AF:

0.327

Gnomad4 NFE exome

AF:

0.374

Gnomad4 OTH exome

AF:

0.315

GnomAD4 genome

AF:

0.260

AC:

39624

AN:

152152

Hom.:

6463

Cov.:

AF XY:

0.259

AC XY:

19237

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.0642

Gnomad4 AMR

AF:

0.262

Gnomad4 ASJ

AF:

0.332

Gnomad4 EAS

AF:

0.212

Gnomad4 SAS

AF:

0.268

Gnomad4 FIN

AF:

0.313

Gnomad4 NFE

AF:

0.371

Gnomad4 OTH

AF:

0.259

Alfa

AF:

0.276

Hom.:

1591

Bravo

AF:

0.246

Asia WGS

AF:

0.203

AC:

707

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.3

DANN

Benign

0.24

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