chr10-22541950-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005028.5(PIP4K2A):āc.890A>Gā(p.Asp297Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,840 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 (ā ).
Frequency
Consequence
NM_005028.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIP4K2A | NM_005028.5 | c.890A>G | p.Asp297Gly | missense_variant | 8/10 | ENST00000376573.9 | NP_005019.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIP4K2A | ENST00000376573.9 | c.890A>G | p.Asp297Gly | missense_variant | 8/10 | 1 | NM_005028.5 | ENSP00000365757 | P1 | |
PIP4K2A | ENST00000545335.5 | c.713A>G | p.Asp238Gly | missense_variant | 8/10 | 2 | ENSP00000442098 | |||
PIP4K2A | ENST00000323883.11 | c.470A>G | p.Asp157Gly | missense_variant | 6/8 | 2 | ENSP00000326294 | |||
PIP4K2A | ENST00000604912.1 | downstream_gene_variant | 2 | ENSP00000473858 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251344Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135834
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461762Hom.: 0 Cov.: 33 AF XY: 0.0000220 AC XY: 16AN XY: 727186
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.890A>G (p.D297G) alteration is located in exon 8 (coding exon 8) of the PIP4K2A gene. This alteration results from a A to G substitution at nucleotide position 890, causing the aspartic acid (D) at amino acid position 297 to be replaced by a glycine (G). 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