Variant 3-27290686-T-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.1674A>G(p.Gly558Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 1,606,012 control chromosomes in the GnomAD database, including 79,244 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 15810 hom., cov: 33)

Exomes 𝑓: 0.28 ( 63434 hom. )

Consequence

NEK10
NM_001394966.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.197

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=-0.53).

BP6

Variant 3-27290686-T-C is Benign according to our data. Variant chr3-27290686-T-C is described in ClinVar as [Benign]. Clinvar id is 1325896.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.197 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 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.1674A>G	p.Gly558Gly	synonymous_variant	19/36	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.1674A>G	p.Gly558Gly	synonymous_variant	19/36		NM_001394966.1	ENSP00000509472.1		A0A8I5KTB8

Frequencies

GnomAD3 genomes

AF:

0.399

AC:

60634

AN:

151998

Hom.:

15767

Cov.:

show subpopulations

Gnomad AFR

AF:

0.752

Gnomad AMI

AF:

0.210

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.167

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.262

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.275

Gnomad OTH

AF:

0.355

GnomAD3 exomes

AF:

0.277

AC:

68327

AN:

246924

Hom.:

11732

AF XY:

0.266

AC XY:

35747

AN XY:

134184

show subpopulations

Gnomad AFR exome

AF:

0.770

Gnomad AMR exome

AF:

0.251

Gnomad ASJ exome

AF:

0.227

Gnomad EAS exome

AF:

0.149

Gnomad SAS exome

AF:

0.202

Gnomad FIN exome

AF:

0.251

Gnomad NFE exome

AF:

0.267

Gnomad OTH exome

AF:

0.273

GnomAD4 exome

AF:

0.282

AC:

410149

AN:

1453894

Hom.:

63434

Cov.:

AF XY:

0.277

AC XY:

200476

AN XY:

723658

show subpopulations

Gnomad4 AFR exome

AF:

0.772

Gnomad4 AMR exome

AF:

0.256

Gnomad4 ASJ exome

AF:

0.231

Gnomad4 EAS exome

AF:

0.170

Gnomad4 SAS exome

AF:

0.205

Gnomad4 FIN exome

AF:

0.244

Gnomad4 NFE exome

AF:

0.281

Gnomad4 OTH exome

AF:

0.297

GnomAD4 genome

AF:

0.399

AC:

60739

AN:

152118

Hom.:

15810

Cov.:

AF XY:

0.391

AC XY:

29046

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.752

Gnomad4 AMR

AF:

0.282

Gnomad4 ASJ

AF:

0.238

Gnomad4 EAS

AF:

0.167

Gnomad4 SAS

AF:

0.214

Gnomad4 FIN

AF:

0.262

Gnomad4 NFE

AF:

0.275

Gnomad4 OTH

AF:

0.354

Alfa

AF:

0.324

Hom.:

5623

Bravo

AF:

0.420

Asia WGS

AF:

0.278

AC:

967

AN:

3474

EpiCase

AF:

0.257

EpiControl

AF:

0.266

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

-0.53

CADD

Benign

8.1

DANN

Benign

0.75

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