chr3-131212815-A-G

Variant names:

• chr3-131212815-A-G
• rs1400014
• NM_024800.5:c.1400-15713A>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.1400-15713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,156 control chromosomes in the GnomAD database, including 55,786 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 0.85 (55786 hom., cov: 32)
• Consequence: NEK11 NM_024800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.887 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.1400-15713A>G		intron	N/A	NP_079076.3
	NEK11	NM_001321221.2		c.1526-15713A>G		intron	N/A	NP_001308150.1
	NEK11	NM_001353022.2		c.1526-15713A>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.1400-15713A>G		intron	N/A	ENSP00000372857.4
	NEK11	ENST00000510688.5	TSL:1	c.1400-15713A>G		intron	N/A	ENSP00000423458.1
	NEK11	ENST00000508196.5	TSL:2	c.1400-15713A>G		intron	N/A	ENSP00000421851.1

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129612 AN: 152036 Hom.: 55741 Cov.: 32

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.852 AC: 129711 AN: 152156 Hom.: 55786 Cov.: 32 AF XY: 0.846 AC XY: 62946 AN XY: 74384

African (AFR) AF: 0.895 AC: 37139 AN: 41512

American (AMR) AF: 0.772 AC: 11792 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2874 AN: 3470

East Asian (EAS) AF: 0.526 AC: 2723 AN: 5174

South Asian (SAS) AF: 0.895 AC: 4321 AN: 4826

European-Finnish (FIN) AF: 0.832 AC: 8804 AN: 10578

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59345 AN: 68006

Other (OTH) AF: 0.842 AC: 1777 AN: 2110

Alfa AF: 0.871 Hom.: 41730

Bravo AF: 0.842

Asia WGS AF: 0.745 AC: 2591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.42
PhyloP100		-0.79
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: rs1400014; hg19: chr3-130931659;