chr10-97640999-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_018425.4(PI4K2A):c.257C>T(p.Ala86Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000905 in 1,547,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018425.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PI4K2A | NM_018425.4 | c.257C>T | p.Ala86Val | missense_variant | 1/9 | ENST00000370631.4 | NP_060895.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PI4K2A | ENST00000370631.4 | c.257C>T | p.Ala86Val | missense_variant | 1/9 | 1 | NM_018425.4 | ENSP00000359665 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151928Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000621 AC: 9AN: 144958Hom.: 0 AF XY: 0.0000249 AC XY: 2AN XY: 80476
GnomAD4 exome AF: 0.00000860 AC: 12AN: 1395562Hom.: 0 Cov.: 32 AF XY: 0.00000869 AC XY: 6AN XY: 690334
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151928Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74200
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 29, 2024 | The c.257C>T (p.A86V) alteration is located in exon 1 (coding exon 1) of the PI4K2A gene. This alteration results from a C to T substitution at nucleotide position 257, causing the alanine (A) at amino acid position 86 to be replaced by a valine (V). 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