Variant chr3-131133948-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_024800.5(NEK11):c.639G>A(p.Ser213=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 1,607,726 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0014 ( 5 hom. )

Consequence

NEK11
NM_024800.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.80

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 made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 3-131133948-G-A is Benign according to our data. Variant chr3-131133948-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2654151.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.8 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEK11	NM_024800.5 linkuse as main transcript	c.639G>A	p.Ser213=	synonymous_variant	7/18	ENST00000383366.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEK11	ENST00000383366.9 linkuse as main transcript	c.639G>A	p.Ser213=	synonymous_variant	7/18	1	NM_024800.5	P1	Q8NG66-1

Frequencies

GnomAD3 genomes

AF:

0.00130

AC:

197

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000966

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000655

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.00187

Gnomad FIN

AF:

0.000472

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00229

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.00172

AC:

426

AN:

247902

Hom.:

AF XY:

0.00188

AC XY:

252

AN XY:

134048

show subpopulations

Gnomad AFR exome

AF:

0.000310

Gnomad AMR exome

AF:

0.000476

Gnomad ASJ exome

AF:

0.000100

Gnomad EAS exome

AF:

0.000880

Gnomad SAS exome

AF:

0.00312

Gnomad FIN exome

AF:

0.000741

Gnomad NFE exome

AF:

0.00238

Gnomad OTH exome

AF:

0.00182

GnomAD4 exome

AF:

0.00140

AC:

2033

AN:

1455486

Hom.:

Cov.:

AF XY:

0.00151

AC XY:

1090

AN XY:

723826

show subpopulations

Gnomad4 AFR exome

AF:

0.000240

Gnomad4 AMR exome

AF:

0.000587

Gnomad4 ASJ exome

AF:

0.000269

Gnomad4 EAS exome

AF:

0.000329

Gnomad4 SAS exome

AF:

0.00259

Gnomad4 FIN exome

AF:

0.000620

Gnomad4 NFE exome

AF:

0.00146

Gnomad4 OTH exome

AF:

0.00143

GnomAD4 genome

AF:

0.00130

AC:

198

AN:

152240

Hom.:

Cov.:

AF XY:

0.00138

AC XY:

103

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.000120

Gnomad4 AMR

AF:

0.000654

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.000472

Gnomad4 NFE

AF:

0.00229

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00184

Hom.:

Bravo

AF:

0.00108

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

NEK11: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.20

DANN

Benign

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.17

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over