chr12-106067004-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_014840.3(NUAK1):c.1784G>T(p.Arg595Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00171 in 1,614,218 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014840.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUAK1 | NM_014840.3 | c.1784G>T | p.Arg595Leu | missense_variant | 7/7 | ENST00000261402.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUAK1 | ENST00000261402.7 | c.1784G>T | p.Arg595Leu | missense_variant | 7/7 | 1 | NM_014840.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00103 AC: 157AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000910 AC: 228AN: 250506Hom.: 1 AF XY: 0.000965 AC XY: 131AN XY: 135692
GnomAD4 exome AF: 0.00178 AC: 2598AN: 1461876Hom.: 5 Cov.: 30 AF XY: 0.00175 AC XY: 1271AN XY: 727240
GnomAD4 genome ? AF: 0.00103 AC: 157AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.000953 AC XY: 71AN XY: 74486
ClinVar
Submissions by phenotype
NUAK1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 20, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at