Variant chr3-27162561-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000383771.8(NEK10):c.846C>T(p.His282=) variant causes a synonymous change. The variant allele was found at a frequency of 0.256 in 1,613,942 control chromosomes in the GnomAD database, including 55,426 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 4526 hom., cov: 32)

Exomes 𝑓: 0.26 ( 50900 hom. )

Consequence

NEK10
ENST00000383771.8 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.09

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP6

Variant 3-27162561-G-A is Benign according to our data. Variant chr3-27162561-G-A is described in ClinVar as [Benign]. Clinvar id is 1325890.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEK10	NM_001394966.1 linkuse as main transcript	c.2869+140C>T		intron_variant		ENST00000691995.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEK10	ENST00000691995.1 linkuse as main transcript	c.2869+140C>T		intron_variant			NM_001394966.1	P1

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35533

AN:

151992

Hom.:

4527

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.307

Gnomad EAS

AF:

0.0818

Gnomad SAS

AF:

0.300

Gnomad FIN

AF:

0.275

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.266

GnomAD3 exomes

AF:

0.266

AC:

66153

AN:

248678

Hom.:

9497

AF XY:

0.272

AC XY:

36592

AN XY:

134590

show subpopulations

Gnomad AFR exome

AF:

0.129

Gnomad AMR exome

AF:

0.348

Gnomad ASJ exome

AF:

0.313

Gnomad EAS exome

AF:

0.0857

Gnomad SAS exome

AF:

0.303

Gnomad FIN exome

AF:

0.269

Gnomad NFE exome

AF:

0.275

Gnomad OTH exome

AF:

0.269

GnomAD4 exome

AF:

0.258

AC:

377731

AN:

1461832

Hom.:

50900

Cov.:

AF XY:

0.261

AC XY:

189933

AN XY:

727210

show subpopulations

Gnomad4 AFR exome

AF:

0.134

Gnomad4 AMR exome

AF:

0.348

Gnomad4 ASJ exome

AF:

0.310

Gnomad4 EAS exome

AF:

0.0762

Gnomad4 SAS exome

AF:

0.304

Gnomad4 FIN exome

AF:

0.266

Gnomad4 NFE exome

AF:

0.259

Gnomad4 OTH exome

AF:

0.255

GnomAD4 genome

AF:

0.234

AC:

35544

AN:

152110

Hom.:

4526

Cov.:

AF XY:

0.238

AC XY:

17665

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.323

Gnomad4 ASJ

AF:

0.307

Gnomad4 EAS

AF:

0.0822

Gnomad4 SAS

AF:

0.300

Gnomad4 FIN

AF:

0.275

Gnomad4 NFE

AF:

0.267

Gnomad4 OTH

AF:

0.264

Alfa

AF:

0.259

Hom.:

3561

Bravo

AF:

0.231

Asia WGS

AF:

0.189

AC:

659

AN:

3478

EpiCase

AF:

0.293

EpiControl

AF:

0.294

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

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

-0.47

CADD

Benign

DANN

Benign

0.51

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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