rs2230469
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005028.5(PIP4K2A):c.752A>T(p.Asn251Ile) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N251S) has been classified as Likely benign.
Frequency
Consequence
NM_005028.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIP4K2A | NM_005028.5 | c.752A>T | p.Asn251Ile | missense_variant | 7/10 | ENST00000376573.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIP4K2A | ENST00000376573.9 | c.752A>T | p.Asn251Ile | missense_variant | 7/10 | 1 | NM_005028.5 | P1 | |
PIP4K2A | ENST00000545335.5 | c.575A>T | p.Asn192Ile | missense_variant | 7/10 | 2 | |||
PIP4K2A | ENST00000323883.11 | c.332A>T | p.Asn111Ile | missense_variant | 5/8 | 2 | |||
PIP4K2A | ENST00000604912.1 | c.290A>T | p.Asn97Ile | missense_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1451686Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 722760
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at