15-43535155-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394395.1(PPIP5K1):c.3992C>T(p.Ala1331Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,611,724 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 (★).
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.3992C>T | p.Ala1331Val | missense_variant | 32/32 | ENST00000420765.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPIP5K1 | ENST00000420765.6 | c.3992C>T | p.Ala1331Val | missense_variant | 32/32 | 5 | NM_001394395.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000400 AC: 6AN: 150006Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251438Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135892
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461718Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 727174
GnomAD4 genome AF: 0.0000400 AC: 6AN: 150006Hom.: 0 Cov.: 32 AF XY: 0.0000683 AC XY: 5AN XY: 73218
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.3821C>T (p.A1274V) alteration is located in exon 31 (coding exon 29) of the PPIP5K1 gene. This alteration results from a C to T substitution at nucleotide position 3821, causing the alanine (A) at amino acid position 1274 to be replaced by a valine (V). 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