3-27302153-C-T

Position:

• chr3-27302153-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394966.1(NEK10):​c.1029-318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,066 control chromosomes in the GnomAD database, including 33,061 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (33061 hom., cov: 32)
• Consequence: NEK10 NM_001394966.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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	c.1029-318G>A		intron_variant		ENST00000691995.1	NP_001381895.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEK10	ENST00000691995.1	c.1029-318G>A		intron_variant			NM_001394966.1	ENSP00000509472.1
NEK10	ENST00000429845.6	c.1029-318G>A		intron_variant		5		ENSP00000395849.2
NEK10	ENST00000341435.9	c.1029-318G>A		intron_variant		2		ENSP00000343847.5

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96618 AN: 151948 Hom.: 33003 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.625

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.636 AC: 96736 AN: 152066 Hom.: 33061 Cov.: 32 AF XY: 0.632 AC XY: 46963 AN XY: 74332

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.621

Alfa AF: 0.567 Hom.: 6273

Bravo AF: 0.657

Asia WGS AF: 0.463 AC: 1611 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.30

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

Other links and lift over

dbSNP: rs653465; hg19: chr3-27343644;