rs903047

chr3-131033165-A-Gchr3-131033165-A-T

Variant summary

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

The NM_024800.5(NEK11):c.170+3287A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.91 in 152,138 control chromosomes in the GnomAD database, including 63,471 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 0.91 (63471 hom., cov: 31)
• Consequence: NEK11 NM_024800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795

Genes affected

NEK11 (HGNC:18593): (NIMA related kinase 11) This gene encodes a member of the never in mitosis gene A family of kinases. The encoded protein localizes to the nucleoli, and may function with NEK2A in the S-phase checkpoint. The encoded protein appears to play roles in DNA replication and response to genotoxic stress. Alternatively spliced transcript variants have been described.[provided by RefSeq, Mar 2009]

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 (NFE) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEK11	NM_024800.5	c.170+3287A>G		intron_variant		ENST00000383366.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEK11	ENST00000383366.9	c.170+3287A>G		intron_variant		1	NM_024800.5	P1

Frequencies

GnomAD3 genomes AF: 0.910 AC: 138294 AN: 152020 Hom.: 63430 Cov.: 31

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.910 AC: 138387 AN: 152138 Hom.: 63471 Cov.: 31 AF XY: 0.903 AC XY: 67181 AN XY: 74368

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.950

Gnomad4 OTH AF: 0.907

Alfa AF: 0.932 Hom.: 7734

Bravo AF: 0.896

Asia WGS AF: 0.768 AC: 2664 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.38
Dann	Benign	0.49

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: rs903047; hg19: chr3-130752009;