chr10-22714301-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005028.5(PIP4K2A):c.26C>T(p.Ser9Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000734 in 1,608,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005028.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIP4K2A | NM_005028.5 | c.26C>T | p.Ser9Phe | missense_variant | 1/10 | ENST00000376573.9 | |
PIP4K2A | XM_006717450.3 | c.26C>T | p.Ser9Phe | missense_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIP4K2A | ENST00000376573.9 | c.26C>T | p.Ser9Phe | missense_variant | 1/10 | 1 | NM_005028.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 151770Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000527 AC: 13AN: 246848Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133844
GnomAD4 exome AF: 0.0000776 AC: 113AN: 1456940Hom.: 0 Cov.: 32 AF XY: 0.0000869 AC XY: 63AN XY: 724918
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 151770Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74124
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2022 | The c.26C>T (p.S9F) alteration is located in exon 1 (coding exon 1) of the PIP4K2A gene. This alteration results from a C to T substitution at nucleotide position 26, causing the serine (S) at amino acid position 9 to be replaced by a phenylalanine (F). 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