Variant 3-27201554-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.2247C>G(p.Val749Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 1,611,470 control chromosomes in the GnomAD database, including 54,334 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4546 hom., cov: 32)

Exomes 𝑓: 0.26 ( 49788 hom. )

Consequence

NEK10
NM_001394966.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0330

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=-0.48).

BP6

Variant 3-27201554-G-C is Benign according to our data. Variant chr3-27201554-G-C is described in ClinVar as [Benign]. Clinvar id is 1325892.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.033 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.31 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.2247C>G	p.Val749Val	synonymous_variant	25/36	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.2247C>G	p.Val749Val	synonymous_variant	25/36		NM_001394966.1	ENSP00000509472.1		A0A8I5KTB8

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35716

AN:

151922

Hom.:

4546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.0836

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.300

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.271

GnomAD3 exomes

AF:

0.266

AC:

66227

AN:

248608

Hom.:

9448

AF XY:

0.272

AC XY:

36614

AN XY:

134570

show subpopulations

Gnomad AFR exome

AF:

0.135

Gnomad AMR exome

AF:

0.340

Gnomad ASJ exome

AF:

0.332

Gnomad EAS exome

AF:

0.0883

Gnomad SAS exome

AF:

0.306

Gnomad FIN exome

AF:

0.296

Gnomad NFE exome

AF:

0.270

Gnomad OTH exome

AF:

0.269

GnomAD4 exome

AF:

0.255

AC:

372488

AN:

1459430

Hom.:

49788

Cov.:

AF XY:

0.258

AC XY:

187406

AN XY:

726072

show subpopulations

Gnomad4 AFR exome

AF:

0.137

Gnomad4 AMR exome

AF:

0.340

Gnomad4 ASJ exome

AF:

0.329

Gnomad4 EAS exome

AF:

0.0817

Gnomad4 SAS exome

AF:

0.306

Gnomad4 FIN exome

AF:

0.293

Gnomad4 NFE exome

AF:

0.253

Gnomad4 OTH exome

AF:

0.254

GnomAD4 genome

AF:

0.235

AC:

35724

AN:

152040

Hom.:

4546

Cov.:

AF XY:

0.240

AC XY:

17824

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.141

Gnomad4 AMR

AF:

0.317

Gnomad4 ASJ

AF:

0.330

Gnomad4 EAS

AF:

0.0840

Gnomad4 SAS

AF:

0.301

Gnomad4 FIN

AF:

0.300

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.269

Alfa

AF:

0.260

Hom.:

1771

Bravo

AF:

0.230

Asia WGS

AF:

0.183

AC:

639

AN:

3478

EpiCase

AF:

0.287

EpiControl

AF:

0.290

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

-0.48

CADD

Benign

6.7

DANN

Benign

0.75

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

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