dbSNP rs1215597: NUAK1:c.240+120G>T (chr12-106138294-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_014840.3(NUAK1):c.240+120G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 1,356,388 control chromosomes in the GnomAD database, including 150,443 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 0.39 ( 13297 hom., cov: 32)

Exomes 𝑓: 0.47 ( 137146 hom. )

Consequence

NUAK1
NM_014840.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.256

Publications

6 publications found

Variant links:

Genes affected

NUAK1 (HGNC:14311): (NUAK family kinase 1) Enables p53 binding activity and protein serine/threonine kinase activity. Involved in several processes, including protein phosphorylation; regulation of cellular senescence; and regulation of myosin-light-chain-phosphatase activity. Located in cytoplasm; microtubule cytoskeleton; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

NUAK1 links:

Genome browser will be placed here

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=-0.76).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014840.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUAK1	NM_014840.3	MANE Select	c.240+120G>T		intron	N/A	NP_055655.1	O60285-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUAK1	ENST00000261402.7	TSL:1 MANE Select	c.240+120G>T		intron	N/A	ENSP00000261402.2	O60285-1

Frequencies

GnomAD3 genomes

AF:

0.394

AC:

59754

AN:

151808

Hom.:

13298

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.512

Gnomad AMR

AF:

0.486

Gnomad ASJ

AF:

0.440

Gnomad EAS

AF:

0.370

Gnomad SAS

AF:

0.511

Gnomad FIN

AF:

0.512

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.402

GnomAD4 exome

AF:

0.473

AC:

570229

AN:

1204462

Hom.:

137146

AF XY:

0.475

AC XY:

279611

AN XY:

588548

show subpopulations

African (AFR)

AF:

0.167

AC:

4399

AN:

26272

American (AMR)

AF:

0.510

AC:

10245

AN:

20080

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

8019

AN:

18216

East Asian (EAS)

AF:

0.346

AC:

11859

AN:

34278

South Asian (SAS)

AF:

0.516

AC:

31626

AN:

61346

European-Finnish (FIN)

AF:

0.512

AC:

15715

AN:

30716

Middle Eastern (MID)

AF:

0.373

AC:

1453

AN:

3900

European-Non Finnish (NFE)

AF:

0.484

AC:

463702

AN:

958946

Other (OTH)

AF:

0.458

AC:

23211

AN:

50708

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

14355

28709

43064

57418

71773

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13904

27808

41712

55616

69520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.393

AC:

59768

AN:

151926

Hom.:

13297

Cov.:

AF XY:

0.398

AC XY:

29552

AN XY:

74210

show subpopulations

African (AFR)

AF:

0.178

AC:

7368

AN:

41492

American (AMR)

AF:

0.487

AC:

7437

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

1527

AN:

3468

East Asian (EAS)

AF:

0.369

AC:

1895

AN:

5140

South Asian (SAS)

AF:

0.511

AC:

2453

AN:

4804

European-Finnish (FIN)

AF:

0.512

AC:

5385

AN:

10516

Middle Eastern (MID)

AF:

0.323

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.476

AC:

32296

AN:

67914

Other (OTH)

AF:

0.400

AC:

846

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1635

3271

4906

6542

8177

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.454

Hom.:

27288

Bravo

AF:

0.379

Asia WGS

AF:

0.444

AC:

1546

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

9.7

(source)

DANN

Benign

0.88

PhyloP100

-0.26

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over