17-38780531-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_003559.5(PIP4K2B):c.428A>C(p.Tyr143Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,613,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003559.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIP4K2B | ENST00000619039.5 | c.428A>C | p.Tyr143Ser | missense_variant | Exon 4 of 10 | 1 | NM_003559.5 | ENSP00000482548.1 | ||
PIP4K2B | ENST00000617781.1 | n.526A>C | non_coding_transcript_exon_variant | Exon 4 of 8 | 2 | |||||
PIP4K2B | ENST00000617499.1 | c.*22A>C | downstream_gene_variant | 4 | ENSP00000477549.1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251400Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135868
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461758Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727172
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.428A>C (p.Y143S) alteration is located in exon 4 (coding exon 4) of the PIP4K2B gene. This alteration results from a A to C substitution at nucleotide position 428, causing the tyrosine (Y) at amino acid position 143 to be replaced by a serine (S). 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