3-131033165-A-G

Variant names:

• chr3-131033165-A-G
• rs903047
• NM_024800.5:c.170+3287A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024800.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEK11	NM_024800.5	MANE Select	c.170+3287A>G		intron	N/A	NP_079076.3
	NEK11	NM_001321221.2		c.170+3287A>G		intron	N/A	NP_001308150.1
	NEK11	NM_001353022.2		c.170+3287A>G		intron	N/A	NP_001339951.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEK11	ENST00000383366.9	TSL:1 MANE Select	c.170+3287A>G		intron	N/A	ENSP00000372857.4
	NEK11	ENST00000510688.5	TSL:1	c.170+3287A>G		intron	N/A	ENSP00000423458.1
	NEK11	ENST00000507910.5	TSL:1	c.170+3287A>G		intron	N/A	ENSP00000426662.1

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

African (AFR) AF: 0.913 AC: 37908 AN: 41514

American (AMR) AF: 0.822 AC: 12560 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3242 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2866 AN: 5152

South Asian (SAS) AF: 0.911 AC: 4400 AN: 4830

European-Finnish (FIN) AF: 0.927 AC: 9807 AN: 10578

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.950 AC: 64592 AN: 67996

Other (OTH) AF: 0.907 AC: 1917 AN: 2114

Alfa AF: 0.931 Hom.: 8052

Bravo AF: 0.896

Asia WGS AF: 0.768 AC: 2664 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.49
PhyloP100		-0.80
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs903047; hg19: chr3-130752009;