3-131229165-G-T

Position:

• chr3-131229165-G-T

Variant summary

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

The NM_024800.5(NEK11):​c.1560+477G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 152,126 control chromosomes in the GnomAD database, including 1,057 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 0.084 (1057 hom., cov: 31)
• Consequence: NEK11 NM_024800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NEK11	NM_024800.5	c.1560+477G>T		intron_variant		ENST00000383366.9	NP_079076.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEK11	ENST00000383366.9	c.1560+477G>T		intron_variant		1	NM_024800.5	ENSP00000372857	P1

Frequencies

GnomAD3 genomes AF: 0.0836 AC: 12709 AN: 152008 Hom.: 1049 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.0472

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0232

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0838 AC: 12755 AN: 152126 Hom.: 1057 Cov.: 31 AF XY: 0.0821 AC XY: 6108 AN XY: 74388

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.0455

Gnomad4 ASJ AF: 0.0472

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0504

Gnomad4 FIN AF: 0.0165

Gnomad4 NFE AF: 0.0232

Gnomad4 OTH AF: 0.0686

Alfa AF: 0.0326 Hom.: 76

Bravo AF: 0.0942

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.3
DANN	Benign	0.28

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: rs10512802; hg19: chr3-130948009;