15-43535314-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394395.1(PPIP5K1):āc.3833G>Cā(p.Gly1278Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000396 in 1,614,188 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001394395.1 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPIP5K1 | NM_001394395.1 | c.3833G>C | p.Gly1278Ala | missense_variant | 32/32 | ENST00000420765.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPIP5K1 | ENST00000420765.6 | c.3833G>C | p.Gly1278Ala | missense_variant | 32/32 | 5 | NM_001394395.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 250986Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135686
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727248
GnomAD4 genome AF: 0.000197 AC: 30AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | The c.3662G>C (p.G1221A) alteration is located in exon 31 (coding exon 29) of the PPIP5K1 gene. This alteration results from a G to C substitution at nucleotide position 3662, causing the glycine (G) at amino acid position 1221 to be replaced by an alanine (A). 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