rs55635245
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002497.4(NEK2):c.15T>G(p.Ala5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 1,612,816 control chromosomes in the GnomAD database, including 3,426 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.048 ( 253 hom., cov: 33)
Exomes 𝑓: 0.062 ( 3173 hom. )
Consequence
NEK2
NM_002497.4 synonymous
NM_002497.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.135
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant 1-211675465-A-C is Benign according to our data. Variant chr1-211675465-A-C is described in ClinVar as [Benign]. Clinvar id is 403229.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.135 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0967 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEK2 | NM_002497.4 | c.15T>G | p.Ala5= | synonymous_variant | 1/8 | ENST00000366999.9 | |
NEK2 | NM_001204182.2 | c.15T>G | p.Ala5= | synonymous_variant | 1/8 | ||
NEK2 | NM_001204183.2 | c.15T>G | p.Ala5= | synonymous_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEK2 | ENST00000366999.9 | c.15T>G | p.Ala5= | synonymous_variant | 1/8 | 1 | NM_002497.4 | P1 | |
NEK2 | ENST00000540251.5 | c.15T>G | p.Ala5= | synonymous_variant | 1/8 | 1 | |||
NEK2 | ENST00000366998.4 | c.15T>G | p.Ala5= | synonymous_variant | 1/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0475 AC: 7236AN: 152234Hom.: 254 Cov.: 33
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GnomAD3 exomes AF: 0.0573 AC: 14289AN: 249186Hom.: 673 AF XY: 0.0549 AC XY: 7405AN XY: 134868
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GnomAD4 exome AF: 0.0616 AC: 90006AN: 1460464Hom.: 3173 Cov.: 31 AF XY: 0.0605 AC XY: 43936AN XY: 726534
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GnomAD4 genome ? AF: 0.0475 AC: 7238AN: 152352Hom.: 253 Cov.: 33 AF XY: 0.0472 AC XY: 3517AN XY: 74516
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Retinal dystrophy Benign:1
Benign, criteria provided, single submitter | research | Dept Of Ophthalmology, Nagoya University | Oct 01, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at