rs543965909
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_052947.4(ALPK2):c.6499G>A(p.Glu2167Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_052947.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251240Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135778
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461682Hom.: 0 Cov.: 32 AF XY: 0.0000371 AC XY: 27AN XY: 727152
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.6499G>A (p.E2167K) alteration is located in exon 13 (coding exon 12) of the ALPK2 gene. This alteration results from a G to A substitution at nucleotide position 6499, causing the glutamic acid (E) at amino acid position 2167 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