dbSNP rs3088051: ULK1:c.*1102T>C (chr12-131922463-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003565.4(ULK1):c.*1102T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 177,832 control chromosomes in the GnomAD database, including 5,597 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 0.24 ( 4663 hom., cov: 34)

Exomes 𝑓: 0.25 ( 934 hom. )

Consequence

ULK1
NM_003565.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.457

Publications

18 publications found

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 was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ULK1	NM_003565.4 link	c.*1102T>C	3_prime_UTR_variant	Exon 28 of 28	ENST00000321867.6	NP_003556.2	O75385
ULK1	XM_011538798.4 link	c.*1102T>C	3_prime_UTR_variant	Exon 28 of 28		XP_011537100.1
ULK1	XM_011538799.3 link	c.*1102T>C	3_prime_UTR_variant	Exon 28 of 28		XP_011537101.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ULK1	ENST00000321867.6 link	c.*1102T>C		3_prime_UTR_variant	Exon 28 of 28	1	NM_003565.4	ENSP00000324560.3		O75385
ULK1	ENST00000540568.1 link	n.*182T>C		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.236

AC:

35906

AN:

152190

Hom.:

4660

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.260

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.0390

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.240

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.281

GnomAD4 exome

AF:

0.254

AC:

6482

AN:

25524

Hom.:

934

Cov.:

AF XY:

0.261

AC XY:

3654

AN XY:

14002

show subpopulations

African (AFR)

AF:

0.123

AC:

AN:

480

American (AMR)

AF:

0.211

AC:

394

AN:

1868

Ashkenazi Jewish (ASJ)

AF:

0.236

AC:

136

AN:

576

East Asian (EAS)

AF:

0.0274

AC:

AN:

914

South Asian (SAS)

AF:

0.322

AC:

1444

AN:

4488

European-Finnish (FIN)

AF:

0.218

AC:

240

AN:

1102

Middle Eastern (MID)

AF:

0.255

AC:

AN:

European-Non Finnish (NFE)

AF:

0.259

AC:

3853

AN:

14852

Other (OTH)

AF:

0.267

AC:

306

AN:

1146

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

236

472

709

945

1181

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.236

AC:

35912

AN:

152308

Hom.:

4663

Cov.:

AF XY:

0.234

AC XY:

17442

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.145

AC:

6048

AN:

41586

American (AMR)

AF:

0.259

AC:

3965

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.238

AC:

825

AN:

3472

East Asian (EAS)

AF:

0.0393

AC:

204

AN:

5188

South Asian (SAS)

AF:

0.358

AC:

1727

AN:

4830

European-Finnish (FIN)

AF:

0.240

AC:

2549

AN:

10618

Middle Eastern (MID)

AF:

0.364

AC:

107

AN:

294

European-Non Finnish (NFE)

AF:

0.288

AC:

19593

AN:

67998

Other (OTH)

AF:

0.285

AC:

601

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1458

2916

4373

5831

7289

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.266

Hom.:

4286

Bravo

AF:

0.228

Asia WGS

AF:

0.226

AC:

786

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.6

(source)

DANN

Benign

0.46

PhyloP100

0.46

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs3088051

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over