rs716784

chr1-198285259-C-T

Variant summary

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

The NM_133494.3(NEK7):c.589+6198C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,648 control chromosomes in the GnomAD database, including 3,731 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 0.20 (3731 hom., cov: 31)
• Consequence: NEK7 NM_133494.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.705

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEK7	NM_133494.3	c.589+6198C>T		intron_variant		ENST00000367385.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEK7	ENST00000367385.9	c.589+6198C>T		intron_variant		5	NM_133494.3	P1
NEK7	ENST00000538004.5	c.589+6198C>T		intron_variant		1		P1
NEK7	ENST00000493790.1	n.474+6198C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30819 AN: 151530 Hom.: 3723 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.203 AC: 30852 AN: 151648 Hom.: 3731 Cov.: 31 AF XY: 0.207 AC XY: 15368 AN XY: 74070

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.180

Alfa AF: 0.154 Hom.: 984

Bravo AF: 0.212

Asia WGS AF: 0.223 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	9.3
Dann	Benign	0.66

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: rs716784; hg19: chr1-198254389;