Genetic Variant NEK11:c.170+11A>G (chr3-131029889-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_024800.5(NEK11):c.170+11A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 1,611,986 control chromosomes in the GnomAD database, including 128,319 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 0.31 ( 8873 hom., cov: 33)

Exomes 𝑓: 0.40 ( 119446 hom. )

Consequence

NEK11
NM_024800.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.873

Publications

9 publications found

Variant links:

Genes affected

NEK11 (HGNC:18593): (NIMA related kinase 11) This gene encodes a member of the never in mitosis gene A family of kinases. The encoded protein localizes to the nucleoli, and may function with NEK2A in the S-phase checkpoint. The encoded protein appears to play roles in DNA replication and response to genotoxic stress. Alternatively spliced transcript variants have been described.[provided by RefSeq, Mar 2009]

NEK11 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=-0.74).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEK11	NM_024800.5 link	c.170+11A>G		intron_variant	Intron 3 of 17	ENST00000383366.9	NP_079076.3	Q8NG66-1B4DM56

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEK11	ENST00000383366.9 link	c.170+11A>G		intron_variant	Intron 3 of 17	1	NM_024800.5	ENSP00000372857.4		Q8NG66-1

Frequencies

GnomAD3 genomes

AF:

0.307

AC:

46605

AN:

152036

Hom.:

8875

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0757

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.375

Gnomad ASJ

AF:

0.351

Gnomad EAS

AF:

0.248

Gnomad SAS

AF:

0.289

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.419

Gnomad OTH

AF:

0.351

GnomAD2 exomes

AF:

0.358

AC:

89788

AN:

251040

AF XY:

0.365

show subpopulations

Gnomad AFR exome

AF:

0.0694

Gnomad AMR exome

AF:

0.372

Gnomad ASJ exome

AF:

0.341

Gnomad EAS exome

AF:

0.239

Gnomad FIN exome

AF:

0.401

Gnomad NFE exome

AF:

0.418

Gnomad OTH exome

AF:

0.386

GnomAD4 exome

AF:

0.398

AC:

581606

AN:

1459832

Hom.:

119446

Cov.:

AF XY:

0.398

AC XY:

288994

AN XY:

726278

show subpopulations

African (AFR)

AF:

0.0689

AC:

2304

AN:

33452

American (AMR)

AF:

0.372

AC:

16648

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.344

AC:

8983

AN:

26108

East Asian (EAS)

AF:

0.284

AC:

11275

AN:

39682

South Asian (SAS)

AF:

0.318

AC:

27383

AN:

86210

European-Finnish (FIN)

AF:

0.400

AC:

21325

AN:

53340

Middle Eastern (MID)

AF:

0.487

AC:

2803

AN:

5760

European-Non Finnish (NFE)

AF:

0.421

AC:

467870

AN:

1110228

Other (OTH)

AF:

0.381

AC:

23015

AN:

60330

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

16325

32651

48976

65302

81627

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14046

28092

42138

56184

70230

<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:

0.306

AC:

46600

AN:

152154

Hom.:

8873

Cov.:

AF XY:

0.307

AC XY:

22807

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0756

AC:

3138

AN:

41524

American (AMR)

AF:

0.374

AC:

5728

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.351

AC:

1218

AN:

3472

East Asian (EAS)

AF:

0.248

AC:

1282

AN:

5172

South Asian (SAS)

AF:

0.291

AC:

1401

AN:

4816

European-Finnish (FIN)

AF:

0.398

AC:

4208

AN:

10566

Middle Eastern (MID)

AF:

0.480

AC:

141

AN:

294

European-Non Finnish (NFE)

AF:

0.419

AC:

28457

AN:

67986

Other (OTH)

AF:

0.346

AC:

731

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1556

3112

4668

6224

7780

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

468

936

1404

1872

2340

<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:

0.363

Hom.:

8011

Bravo

AF:

0.295

Asia WGS

AF:

0.239

AC:

832

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

9.8

(source)

DANN

Benign

0.71

PhyloP100

0.87

PromoterAI

-0.018

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over