Variant 3-27256325-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001394966.1(NEK10):c.2061C>G(p.Thr687Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 1,559,310 control chromosomes in the GnomAD database, including 236,977 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.64 ( 33074 hom., cov: 32)

Exomes 𝑓: 0.53 ( 203903 hom. )

Consequence

NEK10
NM_001394966.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.61

Variant links:

Genes affected

NEK10 (HGNC:18592): (NIMA related kinase 10) Enables protein kinase activity. Involved in several processes, including mucociliary clearance; positive regulation of protein phosphorylation; and regulation of ERK1 and ERK2 cascade. Part of protein kinase complex. Implicated in primary ciliary dyskinesia 44. [provided by Alliance of Genome Resources, Apr 2022]

NEK10 links:

NEK10 (HGNC:):

NEK10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 3-27256325-G-C is Benign according to our data. Variant chr3-27256325-G-C is described in ClinVar as [Benign]. Clinvar id is 1325893.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.62 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NEK10	NM_001394966.1 linkuse as main transcript	c.2061C>G	p.Thr687Thr	synonymous_variant	23/36	ENST00000691995.1	NP_001381895.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEK10	ENST00000691995.1 linkuse as main transcript	c.2061C>G	p.Thr687Thr	synonymous_variant	23/36		NM_001394966.1	ENSP00000509472.1		A0A8I5KTB8

Frequencies

GnomAD3 genomes

AF:

0.635

AC:

96514

AN:

151934

Hom.:

33012

Cov.:

show subpopulations

Gnomad AFR

AF:

0.905

Gnomad AMI

AF:

0.558

Gnomad AMR

AF:

0.623

Gnomad ASJ

AF:

0.571

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.495

Gnomad FIN

AF:

0.537

Gnomad MID

AF:

0.631

Gnomad NFE

AF:

0.535

Gnomad OTH

AF:

0.626

GnomAD3 exomes

AF:

0.531

AC:

114036

AN:

214942

Hom.:

32459

AF XY:

0.524

AC XY:

61421

AN XY:

117258

show subpopulations

Gnomad AFR exome

AF:

0.912

Gnomad AMR exome

AF:

0.613

Gnomad ASJ exome

AF:

0.552

Gnomad EAS exome

AF:

0.199

Gnomad SAS exome

AF:

0.482

Gnomad FIN exome

AF:

0.520

Gnomad NFE exome

AF:

0.523

Gnomad OTH exome

AF:

0.525

GnomAD4 exome

AF:

0.530

AC:

746169

AN:

1407258

Hom.:

203903

Cov.:

AF XY:

0.528

AC XY:

369475

AN XY:

699918

show subpopulations

Gnomad4 AFR exome

AF:

0.924

Gnomad4 AMR exome

AF:

0.622

Gnomad4 ASJ exome

AF:

0.558

Gnomad4 EAS exome

AF:

0.222

Gnomad4 SAS exome

AF:

0.492

Gnomad4 FIN exome

AF:

0.514

Gnomad4 NFE exome

AF:

0.528

Gnomad4 OTH exome

AF:

0.545

GnomAD4 genome

AF:

0.636

AC:

96638

AN:

152052

Hom.:

33074

Cov.:

AF XY:

0.631

AC XY:

46900

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.906

Gnomad4 AMR

AF:

0.623

Gnomad4 ASJ

AF:

0.571

Gnomad4 EAS

AF:

0.221

Gnomad4 SAS

AF:

0.497

Gnomad4 FIN

AF:

0.537

Gnomad4 NFE

AF:

0.535

Gnomad4 OTH

AF:

0.621

Alfa

AF:

0.565

Hom.:

8214

Bravo

AF:

0.656

Asia WGS

AF:

0.449

AC:

1561

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Ciliary dyskinesia, primary, 44

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.22

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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