rs1886541
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_110306.1(LOC101929657):n.3344A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0156 in 152,554 control chromosomes in the GnomAD database, including 73 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 0.016 ( 73 hom., cov: 32)
Exomes 𝑓: 0.021 ( 0 hom. )
Consequence
LOC101929657
NR_110306.1 non_coding_transcript_exon
NR_110306.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0640
Genes affected
NEK3 (HGNC:7746): (NIMA related kinase 3) This gene encodes a member of the NimA (never in mitosis A) family of serine/threonine protein kinases. The encoded protein differs from other NimA family members in that it is not cell cycle regulated and is found primarily in the cytoplasm. The kinase is activated by prolactin stimulation, leading to phosphorylation of VAV2 guanine nucleotide exchange factor, paxillin, and activation of the RAC1 GTPase. Two functional alleles for this gene have been identified in humans. The reference genome assembly (GRCh38) represents a functional allele that is associated with the inclusion of an additional coding exon in protein-coding transcripts, compared to an alternate functional allele that lacks the exon. [provided by RefSeq, Sep 2019]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0771 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC101929657 | NR_110306.1 | n.3344A>G | non_coding_transcript_exon_variant | 2/2 | |||
NEK3 | NM_002498.3 | downstream_gene_variant | ENST00000610828.5 | ||||
NEK3 | NM_152720.3 | downstream_gene_variant | |||||
NEK3 | NR_164641.1 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000613982.1 | n.3348A>G | non_coding_transcript_exon_variant | 2/2 | 1 | |||||
NEK3 | ENST00000610828.5 | downstream_gene_variant | 1 | NM_002498.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0156 AC: 2375AN: 152194Hom.: 74 Cov.: 32
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GnomAD4 exome AF: 0.0207 AC: 5AN: 242Hom.: 0 Cov.: 0 AF XY: 0.0339 AC XY: 4AN XY: 118
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GnomAD4 genome ? AF: 0.0156 AC: 2380AN: 152312Hom.: 73 Cov.: 32 AF XY: 0.0164 AC XY: 1225AN XY: 74478
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at