3-131229165-G-T

Variant names:

• chr3-131229165-G-T
• rs10512802
• NM_024800.5:c.1560+477G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.99).
• 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 rank	MANE	Protein	UniProt
NEK11	NM_024800.5	c.1560+477G>T		intron_variant	Intron 15 of 17	ENST00000383366.9	NP_079076.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEK11	ENST00000383366.9	c.1560+477G>T		intron_variant	Intron 15 of 17	1	NM_024800.5	ENSP00000372857.4

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

African (AFR) AF: 0.219 AC: 9090 AN: 41456

American (AMR) AF: 0.0455 AC: 696 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0472 AC: 164 AN: 3472

East Asian (EAS) AF: 0.115 AC: 593 AN: 5170

South Asian (SAS) AF: 0.0504 AC: 243 AN: 4826

European-Finnish (FIN) AF: 0.0165 AC: 175 AN: 10614

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0232 AC: 1577 AN: 67990

Other (OTH) AF: 0.0686 AC: 145 AN: 2114

Alfa AF: 0.0402 Hom.: 135

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
PhyloP100		1.5
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: rs10512802; hg19: chr3-130948009;