Variant 17-28729008-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_178170.3(NEK8):c.47+148C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0964 in 726,040 control chromosomes in the GnomAD database, including 3,881 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 819 hom., cov: 33)

Exomes 𝑓: 0.095 ( 3062 hom. )

Consequence

NEK8
NM_178170.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.504

Variant links:

Genes affected

NEK8 (HGNC:13387): (NIMA related kinase 8) This gene encodes a member of the serine/threionine protein kinase family related to NIMA (never in mitosis, gene A) of Aspergillus nidulans. The encoded protein may play a role in cell cycle progression from G2 to M phase. Mutations in the related mouse gene are associated with a disease phenotype that closely parallels the juvenile autosomal recessive form of polycystic kidney disease in humans. [provided by RefSeq, Jul 2008]

NEK8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 17-28729008-C-T is Benign according to our data. Variant chr17-28729008-C-T is described in ClinVar as [Benign]. Clinvar id is 1296813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEK8	NM_178170.3 linkuse as main transcript	c.47+148C>T		intron_variant		ENST00000268766.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEK8	ENST00000268766.11 linkuse as main transcript	c.47+148C>T		intron_variant		1	NM_178170.3	P1

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15398

AN:

152206

Hom.:

818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.0844

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.0773

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.0862

Gnomad OTH

AF:

0.0989

GnomAD4 exome

AF:

0.0951

AC:

54563

AN:

573716

Hom.:

3062

AF XY:

0.0972

AC XY:

29461

AN XY:

303210

show subpopulations

Gnomad4 AFR exome

AF:

0.127

Gnomad4 AMR exome

AF:

0.0649

Gnomad4 ASJ exome

AF:

0.131

Gnomad4 EAS exome

AF:

0.162

Gnomad4 SAS exome

AF:

0.147

Gnomad4 FIN exome

AF:

0.0774

Gnomad4 NFE exome

AF:

0.0818

Gnomad4 OTH exome

AF:

0.0930

GnomAD4 genome

AF:

0.101

AC:

15402

AN:

152324

Hom.:

819

Cov.:

AF XY:

0.101

AC XY:

7543

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.0849

Gnomad4 ASJ

AF:

0.132

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.0773

Gnomad4 NFE

AF:

0.0862

Gnomad4 OTH

AF:

0.0983

Alfa

AF:

0.0573

Hom.:

Bravo

AF:

0.102

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

7.3

DANN

Benign

0.72

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over