rs1132816
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_005028.5(PIP4K2A):c.30T>C(p.Ser10Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,608,664 control chromosomes in the GnomAD database, including 62,365 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_005028.5 synonymous
Scores
Clinical Significance
Conservation
Publications
Genome browser will be placed here
ACMG classification
Our verdict: Benign. The variant received -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIP4K2A | NM_005028.5 | c.30T>C | p.Ser10Ser | synonymous_variant | Exon 1 of 10 | ENST00000376573.9 | NP_005019.2 | |
PIP4K2A | XM_006717450.3 | c.30T>C | p.Ser10Ser | synonymous_variant | Exon 1 of 9 | XP_006717513.1 | ||
PIP4K2A | NM_001330062.2 | c.-395T>C | upstream_gene_variant | NP_001316991.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.321 AC: 48556AN: 151294Hom.: 9283 Cov.: 30 show subpopulations
GnomAD2 exomes AF: 0.247 AC: 60081AN: 243608 AF XY: 0.247 show subpopulations
GnomAD4 exome AF: 0.262 AC: 381471AN: 1457252Hom.: 53059 Cov.: 33 AF XY: 0.261 AC XY: 189544AN XY: 725108 show subpopulations
GnomAD4 genome AF: 0.321 AC: 48628AN: 151412Hom.: 9306 Cov.: 30 AF XY: 0.312 AC XY: 23095AN XY: 74014 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at