rs552647
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394966.1(NEK10):c.490-48G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 1,134,696 control chromosomes in the GnomAD database, including 174,947 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 0.64 ( 33043 hom., cov: 32)
Exomes 𝑓: 0.53 ( 141904 hom. )
Consequence
NEK10
NM_001394966.1 intron
NM_001394966.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.221
Genes affected
NEK10 (HGNC:18592): (NIMA related kinase 10) Enables protein kinase activity. Involved in several processes, including mucociliary clearance; positive regulation of protein phosphorylation; and regulation of ERK1 and ERK2 cascade. Part of protein kinase complex. Implicated in primary ciliary dyskinesia 44. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEK10 | NM_001394966.1 | c.490-48G>T | intron_variant | ENST00000691995.1 | NP_001381895.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEK10 | ENST00000691995.1 | c.490-48G>T | intron_variant | NM_001394966.1 | ENSP00000509472 | P1 | ||||
NEK10 | ENST00000341435.9 | c.490-48G>T | intron_variant | 2 | ENSP00000343847 | |||||
NEK10 | ENST00000429845.6 | c.490-48G>T | intron_variant | 5 | ENSP00000395849 | |||||
NEK10 | ENST00000491627.1 | n.693-48G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.635 AC: 96552AN: 151974Hom.: 32987 Cov.: 32
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GnomAD3 exomes AF: 0.551 AC: 94206AN: 170998Hom.: 27270 AF XY: 0.543 AC XY: 50529AN XY: 93026
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GnomAD4 exome AF: 0.527 AC: 517852AN: 982604Hom.: 141904 Cov.: 12 AF XY: 0.525 AC XY: 261732AN XY: 498628
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GnomAD4 genome AF: 0.636 AC: 96668AN: 152092Hom.: 33043 Cov.: 32 AF XY: 0.631 AC XY: 46929AN XY: 74338
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at