rs781479336
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_058004.4(PI4KA):c.5977G>A(p.Asp1993Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_058004.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152114Hom.: 0 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000288 AC: 42AN: 1460396Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 726572
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152114Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74292
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.5977G>A (p.D1993N) alteration is located in exon 52 (coding exon 52) of the PI4KA gene. This alteration results from a G to A substitution at nucleotide position 5977, causing the aspartic acid (D) at amino acid position 1993 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
PI4KA: PM2, PP2, PP3 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at