chr1-211658657-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The ENST00000540251.5(NEK2):c.1167G>A(p.Ter389=) variant causes a stop retained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000428 in 413,578 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00029 ( 0 hom., cov: 29)
Exomes 𝑓: 0.00048 ( 2 hom. )
Consequence
NEK2
ENST00000540251.5 stop_retained
ENST00000540251.5 stop_retained
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.758
Genes affected
NEK2 (HGNC:7745): (NIMA related kinase 2) This gene encodes a serine/threonine-protein kinase that is involved in mitotic regulation. This protein is localized to the centrosome, and undetectable during G1 phase, but accumulates progressively throughout the S phase, reaching maximal levels in late G2 phase. Alternatively spliced transcript variants encoding different isoforms with distinct C-termini have been noted for this gene. [provided by RefSeq, Feb 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.05).
BP6
?
Variant 1-211658657-C-T is Benign according to our data. Variant chr1-211658657-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3046446.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.758 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEK2 | NM_001204182.2 | c.1167G>A | p.Ter389= | stop_retained_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEK2 | ENST00000540251.5 | c.1167G>A | p.Ter389= | stop_retained_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000295 AC: 36AN: 121960Hom.: 0 Cov.: 29
GnomAD3 genomes
?
AF:
AC:
36
AN:
121960
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000376 AC: 44AN: 117006Hom.: 0 AF XY: 0.000509 AC XY: 33AN XY: 64794
GnomAD3 exomes
AF:
AC:
44
AN:
117006
Hom.:
AF XY:
AC XY:
33
AN XY:
64794
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000484 AC: 141AN: 291534Hom.: 2 Cov.: 0 AF XY: 0.000646 AC XY: 108AN XY: 167178
GnomAD4 exome
AF:
AC:
141
AN:
291534
Hom.:
Cov.:
0
AF XY:
AC XY:
108
AN XY:
167178
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000295 AC: 36AN: 122044Hom.: 0 Cov.: 29 AF XY: 0.000389 AC XY: 22AN XY: 56530
GnomAD4 genome
?
AF:
AC:
36
AN:
122044
Hom.:
Cov.:
29
AF XY:
AC XY:
22
AN XY:
56530
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
NEK2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 07, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at