chr5-103201584-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001276277.3(PPIP5K2):āc.3682A>Gā(p.Ser1228Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0423 in 1,610,884 control chromosomes in the GnomAD database, including 1,709 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001276277.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0306 AC: 4654AN: 152126Hom.: 109 Cov.: 32
GnomAD3 exomes AF: 0.0303 AC: 7548AN: 249112Hom.: 180 AF XY: 0.0308 AC XY: 4143AN XY: 134688
GnomAD4 exome AF: 0.0435 AC: 63432AN: 1458642Hom.: 1600 Cov.: 31 AF XY: 0.0424 AC XY: 30730AN XY: 725604
GnomAD4 genome AF: 0.0306 AC: 4655AN: 152242Hom.: 109 Cov.: 32 AF XY: 0.0300 AC XY: 2230AN XY: 74422
ClinVar
Submissions by phenotype
PPIP5K2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 11, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | This variant is associated with the following publications: (PMID: 31118516, 24464100, 27398621) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at