chr15-43535140-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394395.1(PPIP5K1):c.4007G>T(p.Cys1336Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,358 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C1336Y) has been classified as Uncertain significance.
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.4007G>T | p.Cys1336Phe | missense_variant | 32/32 | ENST00000420765.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPIP5K1 | ENST00000420765.6 | c.4007G>T | p.Cys1336Phe | missense_variant | 32/32 | 5 | NM_001394395.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000726 AC: 11AN: 151512Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251478Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135912
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727224
GnomAD4 genome AF: 0.0000726 AC: 11AN: 151512Hom.: 0 Cov.: 32 AF XY: 0.0000811 AC XY: 6AN XY: 74004
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at