1-198199889-A-G

Position:

• chr1-198199889-A-G

Variant summary

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

The NM_133494.3(NEK7):​c.-28-32664A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,056 control chromosomes in the GnomAD database, including 1,071 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 0.10 (1071 hom., cov: 32)
• Consequence: NEK7 NM_133494.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

Genes affected

NEK7 (HGNC:13386): (NIMA related kinase 7) NIMA-related kinases share high amino acid sequence identity with the gene product of the Aspergillus nidulans 'never in mitosis A' gene, which controls initiation of mitosis.[supplied by OMIM, Jul 2002]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NEK7	NM_133494.3	c.-28-32664A>G		intron_variant		ENST00000367385.9	NP_598001.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEK7	ENST00000367385.9	c.-28-32664A>G		intron_variant		5	NM_133494.3	ENSP00000356355.4
NEK7	ENST00000538004.5	c.-28-32664A>G		intron_variant		1		ENSP00000444621.1
NEK7	ENST00000367383.5	c.-28-32664A>G		intron_variant		2		ENSP00000356353.1
NEK7	ENST00000442588.5	c.-140-21110A>G		intron_variant		5		ENSP00000392745.1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15222 AN: 151938 Hom.: 1064 Cov.: 32

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0641

Gnomad EAS AF: 0.0921

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0890

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.100 AC: 15246 AN: 152056 Hom.: 1071 Cov.: 32 AF XY: 0.106 AC XY: 7884 AN XY: 74316

Gnomad4 AFR AF: 0.0562

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.0641

Gnomad4 EAS AF: 0.0920

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0890

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0607 Hom.: 131

Bravo AF: 0.104

Asia WGS AF: 0.181 AC: 631 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.29

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: rs2884765; hg19: chr1-198169019;