rs10861554
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014840.3(NUAK1):c.580-3548T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,998 control chromosomes in the GnomAD database, including 19,901 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 0.50 ( 19901 hom., cov: 32)
Consequence
NUAK1
NM_014840.3 intron
NM_014840.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.46
Genes affected
NUAK1 (HGNC:14311): (NUAK family kinase 1) Enables p53 binding activity and protein serine/threonine kinase activity. Involved in several processes, including protein phosphorylation; regulation of cellular senescence; and regulation of myosin-light-chain-phosphatase activity. Located in cytoplasm; microtubule cytoskeleton; and nuclear lumen. [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=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUAK1 | NM_014840.3 | c.580-3548T>G | intron_variant | ENST00000261402.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUAK1 | ENST00000261402.7 | c.580-3548T>G | intron_variant | 1 | NM_014840.3 | P1 | |||
NUAK1 | ENST00000548902.1 | c.187-3548T>G | intron_variant | 4 | |||||
NUAK1 | ENST00000549704.1 | c.-171-3548T>G | intron_variant | 4 | |||||
NUAK1 | ENST00000553094.1 | c.-24+7473T>G | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.503 AC: 76371AN: 151880Hom.: 19880 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.503 AC: 76437AN: 151998Hom.: 19901 Cov.: 32 AF XY: 0.509 AC XY: 37789AN XY: 74280
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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