chr12-106067435-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_014840.3(NUAK1):c.1353G>A(p.Pro451=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00445 in 1,614,144 control chromosomes in the GnomAD database, including 89 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 46 hom., cov: 33)
Exomes 𝑓: 0.0033 ( 43 hom. )
Consequence
NUAK1
NM_014840.3 synonymous
NM_014840.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -8.06
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
?
Variant 12-106067435-C-T is Benign according to our data. Variant chr12-106067435-C-T is described in ClinVar as [Benign]. Clinvar id is 779952.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-8.06 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.015 (2290/152252) while in subpopulation AFR AF= 0.0443 (1842/41536). AF 95% confidence interval is 0.0427. There are 46 homozygotes in gnomad4. There are 1084 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 45 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUAK1 | NM_014840.3 | c.1353G>A | p.Pro451= | synonymous_variant | 7/7 | ENST00000261402.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUAK1 | ENST00000261402.7 | c.1353G>A | p.Pro451= | synonymous_variant | 7/7 | 1 | NM_014840.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0150 AC: 2282AN: 152134Hom.: 45 Cov.: 33
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GnomAD3 exomes AF: 0.00754 AC: 1894AN: 251340Hom.: 26 AF XY: 0.00637 AC XY: 865AN XY: 135838
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GnomAD4 exome AF: 0.00334 AC: 4886AN: 1461892Hom.: 43 Cov.: 33 AF XY: 0.00325 AC XY: 2365AN XY: 727248
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GnomAD4 genome ? AF: 0.0150 AC: 2290AN: 152252Hom.: 46 Cov.: 33 AF XY: 0.0146 AC XY: 1084AN XY: 74446
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 18, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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