chr1-205303484-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030952.3(NUAK2):c.1853G>A(p.Arg618Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000249 in 1,604,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030952.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUAK2 | NM_030952.3 | c.1853G>A | p.Arg618Gln | missense_variant | Exon 7 of 7 | ENST00000367157.6 | NP_112214.3 | |
NUAK2 | XM_047431309.1 | c.1457G>A | p.Arg486Gln | missense_variant | Exon 6 of 6 | XP_047287265.1 | ||
NUAK2 | XM_005245515.5 | c.1112G>A | p.Arg371Gln | missense_variant | Exon 3 of 3 | XP_005245572.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000330 AC: 8AN: 242456Hom.: 0 AF XY: 0.0000306 AC XY: 4AN XY: 130932
GnomAD4 exome AF: 0.0000165 AC: 24AN: 1452272Hom.: 0 Cov.: 29 AF XY: 0.0000166 AC XY: 12AN XY: 721972
GnomAD4 genome AF: 0.000105 AC: 16AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1853G>A (p.R618Q) alteration is located in exon 7 (coding exon 7) of the NUAK2 gene. This alteration results from a G to A substitution at nucleotide position 1853, causing the arginine (R) at amino acid position 618 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at