1-198199889-A-G

Variant names:

• chr1-198199889-A-G
• rs2884765
• NM_133494.3:c.-28-32664A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_133494.3. 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
	NEK7	NM_133494.3	MANE Select	c.-28-32664A>G		intron	N/A	NP_598001.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEK7	ENST00000367385.9	TSL:5 MANE Select	c.-28-32664A>G		intron	N/A	ENSP00000356355.4
	NEK7	ENST00000538004.5	TSL:1	c.-28-32664A>G		intron	N/A	ENSP00000444621.1
	NEK7	ENST00000367383.5	TSL:2	c.-28-32664A>G		intron	N/A	ENSP00000356353.1

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

African (AFR) AF: 0.0562 AC: 2332 AN: 41514

American (AMR) AF: 0.217 AC: 3322 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0641 AC: 222 AN: 3466

East Asian (EAS) AF: 0.0920 AC: 476 AN: 5176

South Asian (SAS) AF: 0.252 AC: 1216 AN: 4818

European-Finnish (FIN) AF: 0.122 AC: 1286 AN: 10500

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0890 AC: 6052 AN: 67986

Other (OTH) AF: 0.129 AC: 273 AN: 2110

Alfa AF: 0.0710 Hom.: 192

Bravo AF: 0.104

Asia WGS AF: 0.181 AC: 631 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.29
PhyloP100		-2.5
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: rs2884765; hg19: chr1-198169019;