6-33722856-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_054111.5(IP6K3):c.1097G>A(p.Arg366His) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,613,584 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R366C) has been classified as Uncertain significance.
Frequency
Consequence
NM_054111.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251408Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135886
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461496Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727074
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1097G>A (p.R366H) alteration is located in exon 7 (coding exon 5) of the IP6K3 gene. This alteration results from a G to A substitution at nucleotide position 1097, causing the arginine (R) at amino acid position 366 to be replaced by a histidine (H). 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