NM_001205019.2:c.146G>A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS2_Supporting
The NM_001205019.2(GK):c.146G>A(p.Arg49Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000464 in 1,078,118 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. 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 Uncertain significance (★).
Frequency
Consequence
NM_001205019.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112400Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34566
GnomAD4 exome AF: 0.00000414 AC: 4AN: 965718Hom.: 0 Cov.: 19 AF XY: 0.00000731 AC XY: 2AN XY: 273604
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112400Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34566
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.146G>A (p.R49K) alteration is located in exon 2 (coding exon 2) of the GK gene. This alteration results from a G to A substitution at nucleotide position 146, causing the arginine (R) at amino acid position 49 to be replaced by a lysine (K). 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